Bits and Pieces, 10 Most authors of Bits and Pieces will make available listings and/or machine-readable versions of their proprams. Please read each description carefully to determine &mpatihility with your own computing environment before requesting materials from any of the authors. Revised guidelines for authors of Bits and Pieces appeared in the February 1982 issue of T H E JOURNAL.
Molecular Input to a Computer and E. F. Meyer, Jr. Department of Biochemistry and Biophysics Texas A & M University. College Station. TX 77843 W. G. White, S. M. Swanson,
Even though the use of computers in chemistry appears to he in an expansive phase, a gap generally exists in that the chemist and computer frequently are able to communicate only in terms of numbers, rather than from sketches of molecular structures. The frequently used FROM ( I ) or TO (2) or matrix (3) notations do not describe a molecule in a way natural to the chemist and his sketches. Moreover, such a description is two-dimensional until additional information is given. We, therefore, have interfaced a moderately priced data tablet (Summaeravhics Coro. BITPAD) to our lahoratorv is also attached a vecto; minicomputer, : ~ ~ ~ 1 1 / 4 0 which , General 3DM monitor. However, for the purposes described here, a Tektronix or similar CRT display would he sufficient. Proeram PAD i n t e r ~ r e t sthe digital outvut from the tahlet to create a numeric a i d topographical map that a chemist can immediatelv recoenize as the molecule being drawn. The chemist uses a halfpoint stylus to specify the a6mic positions in the sketch. Program PAD accepts the numeric signals from the BITPAD, stores the locations, and generates a display command so that each new atom and hond appear immediately on the CRT screen. In the drawing mode, a line (i.e., chemical hond) connects a cruciform symhol with the lastdrawn atom and follows it until the appropriate position is fixed. A menu tahle next to the molecular sketch on the CRT contains label and program control options. Ring closures are made by positioning the cross on the word Ring, then touching the appropriate atoms. Misplaced bonds may he removed, in reverse order, by consecutively touching the word Erase. The menu also contains nnmhen, frequently used atomic symbols, and command words that control the sequence of programs or input/ontput. The default value for all atoms is C (tetrahedral. Z = 6 ) . If the desired atomic svmbol is not availahle. " it may'he i n p k from the keyboard, Execution of vroeram PAD occurs in four nhases (INPUT. ID, REFINE, and GUTPUT). The monitor command to run the vroeram initiates the INPUT vhase. in which the user s he simply draws the molecule (Fig. 1).~ e n u ' c o m m a n d may s~ecifiedwith the stvlns in order to effect erasures.. ring- clos&es, and main-chain branches. In the ID phase, the user points to each atom and then to any of the ID descriptors corresponding to it (Fig. 2). Descriptors are available for atom type (i.e., atomic symbol), bonding geometry (e.g., double hond), and spatial position.
In this second phase, 3-D notation may he input by signalling u p or down with respect to the plane of the neighboring atoms. The REFINE menu command adjusts the approximate atomic positions to an idealized 3-D representation of the molecule with respect to a dictionary of standard hond leneths. (Fie. " , aneles. . . , and torsion aneles " . - 3). All descri~tive information previously input is used to create the 3-D model, usine" an aleorithm hv Dewar (. 4.) . The treatment of rings " currently requires explicit geometric descriptors. The e.r a.~ h i c adisolav l of the model at each step provides a strong teaching rwi an.d reminder concerning the-cho~ceof values being used to overr~dethe default m < k u l n rgeometri~s.Users
ERASE
BREAK
tb
u Figure I . Unretouched screen image during execution of the input module
L I
Figure 2. Screen image during execution of the identification module
Figure 3. Unretouched stereoviewof a model of ATP (adenosinetriphasphate) as drawn and refined by program PAD. VVlume 59
Number 6 June 1982
515
with access to larger computer systems may wish t o refine the model further. Completion of the refmement stage signals commencement of the OUTPUT phase of our program PAD. We use program PAD most frequently to create models of drug and substrate or inhihitor molecules. These models are then fit interactively into the receptor site of proteins and enzymes being investigated by this lahoratory (5).A second use involves the input of molecular structures t o program CHIRAL (6),which a ~ ~ l i the e s Cahn-Ineold-Preloe rules to determine chiral descriptors for stereogenic centers. The method involved in the develo~mentof vrwmm 1'AI) could have a direct auolication to the enormous data entry prohlems faced by chemical documentation moups, with the added benefit that full three-dimensional information may he input; most major chemical documentation efforts employ two-dimensional or vaguely three-dimensional representations, even though very few moleucles are truly flat, and lost information (i.e., dimensions) is difficult to restore at a later step without connidemhle ambiguity. Pnmnm PAD. written in Fortran N for the PDP11140 runs underk~~ll- with a Vector General 3DM display, contains 1149 statements and 151 comments. Execution requires 27100 16-hit words. Documentation includes source listing and thesis (7). Copies of the listing are available far $5; copies of the thesis are $15. Your 800 bpi magnetic tape can be written with FLX (PDP11 and VAX) for $10 uostane & handline. Make check to Biographies ~ahoratory;~ e ~ & t m e of n t~yochemistry and Biophysics, Texas A & M University, College Station, T X 77843. A simplified version of PAD has been written in PASCAL for the Apple I1 computer. A listing is available for $5 at the above address. This work has been generously supported by a grant from the Tektronix Cor~oration.the NIH. the Robert A. Welch Foundation, and tGe Texas kgriculturh Experiment Station. We thank Dr. Alton Banks for orovidine us access to the A ~ n l e I1 computer.
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Calculator Programs for Analyzing TGA Data J. E. House, Jr. lllinOls State University, Normal. IL 61761 Nonisothermal TGA studies have become i m ~ o r t a n for t determining kinetic parameters in all fields of'chemistry. However, analvsis of the data can he laborious and time consuming. The usual rate law is A da = -=-EIRTdT (1) (I-4" B where CY is the fraction reacted, T is the temperature ( K ) ,n is the reaction order, E is the activation energy, A is the frequency factor, and @ is the heating rate (8). Exact integration of the right side of eqn. (1) cannot be accomplished so there are several ao~roximaterate eouations that are used (9). One of themost widely used methods for treating TGA data ia that of Coats and Redfern ( 1 0 ) . In this method. the integrated equations are
when n = 1,and when n
z 1,
The value of a is calculated as an observed mass loss ( D ) divided by that expected for the complete reaction. The term In [(AR/E@)(l- (ZRTIE)] is very nearly constant. If we represent the left-hand side of eqns. (2) and (3) as ~ ( c Ythen ), a linear relationship exists between f ( a ) and 1IT for the correct value of n. T h e n E is found from the slope and A is calculated 518
Journal of Chemical Education
from the intercept. In carrying out the analysis, typical values of n that are of theoretical interest (usually n = 0,1/3,2/3,1, 413,513, and 2) are used and each f ( a ) is computed for each data point (tj,Dj). Linear regression of f ( a ) versus 1IT is then performed. Such computations are laborious and a programmable calculator speeds the analysis of TGA data enormouslv. T W types ~ of programs for programmable calculators have been developed. The first of these, CRPBP, is for use with machines having a limited numher of program steps and memories such as the Hewlett-Packard HP-25 and HP-33. This program involves entering a temperature and deflection (mass loss) data pair (t;,Di). The program then computes sequentially the value off (a) for n = 1,0,113,2/3,413,513, and 2. The next data pair is entered and f(a) computed for all the values of n. When the process is complete for all the data points, these f ( a ) values are used in linear regression or eraohical dottine aeainst 11T. - The second prigram, CRCOM, is for use with the Texas Instruments TI-59 and TI-58 calculators. I t uses 235 program steps and up to 60 memories, depending on the numher of data pairs. Up to 14 (t;.D;) data pairs can he used with the TI-59 and fou; data pairs can he ;sed with the TI-58. The desired f ( a ) values are computed and stored until all the data have been used. Then, linear regression is performed to determine slope, intercept, and correlation coefficient. The value of n is inciemented and the process repeated. The temperature and deflection data are entered only once and the seven values of n are used automatically. The value of n yielding the highest correlation coefficient is assumed to be the correct order. These programs will he useful to students and teachers in instrumental analysis, solid state chemistry, physical chemistrv. r and other amlied lahoratorv areas ...~ o l.v m echemistrv. using thermal analysis. using the pro&m, the analysis of the data takes no longer than obtaining the TGA curve and errors are reduced considerably when compared to computing f ( a ) values point-hy-point. Also, faculty memhers may find the programs useful for verifying students' results obtained by other methods and as a teachinc tool for instruction in data analysis for comparison of TGA ;esults with usual isothermal kinetic data. Finally, the programs allow practice in using hypothetical data in "dry lab" situations without spending a great deal of time in unproductive, repetitive calculator work. Complete listings of the programs and instructions for their use are available from the author a t the address given above. Send $2 (cash or check payable to J. E. House, Jr.) for the CRPBP promam (for HP-25 and HP-33C calculators) or $3 for the ~ R C O M for use with the TI-59 a n d ~ 1 - 5 8 calculators.
Library Orientation to the Technical Literature Patrlcla C. FlaL Paul Smith's College, Paul Smiths, NY 12970 A utility computer program has been developed to provide students in general chemistry with a basic library orientation lahoratory. Employers expect library know-how of our Ecology and Environmental Technology graduates. Several recent articles in THIS JOURNAL. (11-15). further attest to the need to orient students researching technical information in appropriate reference hooks, periodicals, files, or stacks. I use a library "experiment" as the first lab in the second semester of freshman general chemistry, a semester in which there is also a required "research" project which is an independent fact-gathering lab project hacked by a bibliography of material pertinent to the individual projects. Even with freshmen English in their curricula, students are not always able to exhaustively search the technical literature in the library. This "experiment" will help students learn to gather technical information in a systematic, organized manner. I
