Libris Britannia 4/science library(b).zip/science library(b)/CHEMIST/TORG311.ZIP/TORGANAL.DOC

Text File | 1993-02-13 | 15KB | 352 lines

This file contains documentation for the program:-

TORGANAL - a shareware qualitative organic analysis simulation program
       version 3.11, released February 1993

    written by Dr Adrian Blackman
           Chemistry Department
           University of Tasmania




        SECTION A - Disk contents and file description

        SECTION B - Program description

        SECTION C - Hardware requirements and installation

        SECTION D - Revision history

        SECTION E - Registration and payment



---------------------------SECTION A - DISK CONTENTS--------------------------
                  Shareware version

torganal.exe      main program
torganal.ini      contains a few parameters which can be changed (ascii)
mainmenu.txt      text for main menu (ascii)
cclasses.txt      text for pull-down menus (ascii)
unk??.txt         data for each of the unknowns (ascii)
          01-12, 30-44, 60-78
user.txt          data for the user (ascii)
setup.exe         installation program (see section C)
torganal.doc      this file
newuser.exe       generates user.txt files
readme.1st        very brief greetings



-----------------------SECTION B - PROGRAM DESCRIPTION-----------------------

------Why simulate organic qualitative analysis?
 Identification of unknowns plays an important part in most organic chemistry
laboratory courses. Since there are over 8 million compounds and a wide
variety of possible chemical reactions and measurements this can be a
daunting task for a student. To identify an unknown a small number of
reactions and measurements have to be selected in a logical manner, carried
out in the laboratory and then interpreted. Students therefore have an
opportunity to plan a logical approach, use chemical reactions, and obtain
and interpret physical measurements including spectroscopic data. By using a
computer simulation of this process, students are able to discover and
rehearse the strategy of identifying an organic unknown in a situation free
from the additional uncertainties of performing unfamiliar laboratory work
and then relying on the results. Once a logical approach has been developed,
identification of an unknown can be undertaken in the laboratory with more
confidence and efficiency.

------Program design criteria.
Organic compounds are usually identified by first determining the functional
group(s) present and then selecting the correct compound from those listed in
a table of compounds having that functional group.

Functional groups are mostly determined by a combination of chemical tests
and interpretation of spectroscopic data. In fact, with modern spectroscopic
instrumentation yielding a variety of spectra it may be possible to determine
the structure of a compound from this information alone but additional
supplementary data are usually required. Many of the chemical tests (known
as functional group tests) can be logically arranged into a hierarchy where
a more general test is to be done before a more detailed one. A natural
consequence of this is that the more detailed one should only be performed if
the more general one has given a positive result. For example, a test for a
primary amine should only be done if nitrogen has been shown to be present
and should not be attempted if it has been revealed that nitrogen is absent.
Even if there is no prescribed general test, the test in question may be
precluded by the result of another test which has already been disclosed.
The combination of spectral information and chemical tests can be treated in
much the same way. To take an example, it is inappropriate to perform a test
for a ester if this functional group is precluded by an infrared spectrum
which has been revealed.

For most tests there are the following three types of possible responses:-
*  There is a more general test to be completed first which has not been done.
*  The test is precluded by information which has already been revealed.
*  The result of the test is to be given.

A computer program which simulates the process of organic analysis and which
also is to encourage a logical approach should give the appropriate response
for each test at any stage of the analysis and be able to give context
sensitive help if that response is not understood.

Once the compound's class is established (by knowing the functional groups)
the final task is to identify the compound. Tables of compounds are available
- a different one for each class of compound. This task then reduces to
finding a unique match between the unknown's measured chemical and physical
characteristics and those of a compound in these published tables (or other
sources). Data that are used for this purpose include such things as melting
and boiling points of the unknown and melting points of derivatives.

Identification of a unknown organic compound is therefore a combination of
chemical tests, physical measurements including spectral interpretation, and
preparation of derivatives. These are best done in a prescribed sequence with
each stage of the analysis being completed before progression onto the next
one. The following three sequential stages may be defined:-

  Stage 1 - Essential tests. For each unknown there is separately defined a
  set of tests and measurements which are considered essential. Their
  completion should ensure that effort is not wasted in stage 2 making
  incorrect derivatives.

  Stage 2 - Derivative formation. Each unknown has one or more derivatives
  or a spectroscopic equivalent; these are individually defined. Completion
  is required so that random guessing during stage 3 will be minimised.

  Stage 3 - Naming the compound. Most organic compounds have more than one
  name. One of these has to be supplied before the unknown is considered to
  be identified.

A simulation of the process therefore should ensure that each stage of the
analysis is complete before progression onto the next one. Context sensitive
help to explain this should be available if required.


------Program features
"Torganal" - Tasmanian organic analysis, has been developed to meet the
requirements outlined above and is now available for IBM compatible computers
(640K memory and at least EGA graphics are required).

Additional features of the program include:-

*  Responses for about 50 tests and measurements and 40 derivatives are
   available for nearly 50 unknowns.

*  Pull-down menus are used.

*  A short hint about the purpose of each item as it is highlighted is always
   shown on the screen.

*  Background information about what constitutes a positive result for the
   chemical tests can be obtained.

*  A review of all the information which has been revealed may be obtained,
   with or without detailed help about the result for each item.

*  Help about each unknown (as distinct from help about the result of each
   test) can be obtained but its availability is related to the number of
   tests asked for and the group to which the unknown belongs.

*  The analysis may be stopped and continued with at a later stage.

*  The 46 unknowns are available in three groups. Each group of unknowns
   is progressively more difficult but more spectra are available (1H & 13C
   nmr, ir, ms and uv are all accessible for the last group).

*  Unknowns in groups one and two have to be identified by the approach which
   has been outlined above. For pedagogical reasons the hierarchical
   structure and the various prerequisites and stages are rigidly applied.
   This is for the benefit of novices (more experienced users may find this
   restricted approach frustrating). Registered users receive an additional
   program which allows editing of these restrictions if this is required.

*  The unknowns in group three can be identified solely from spectroscopic
   data if required - for these the prerequisites outlined above have been
   somewhat relaxed.

*  Each unknown can be identified by supplying one of usually several
   alternative names. The possible names include the most common trivial
   names and the IUPAC name. Each compound, with its various names, may be
   found in one or more of the following:
    - "Elementary practical organic chemistry. Part 2: qualitative organic
      analysis", AI Vogel, 2nd. ed., 1966, Longmans.
    - "CRC handbook of tables for organic compound identification",
      Z Rappoport, 3rd. ed., 1967, CRC Press.
    - "Dictionary of organic compounds", 5th. ed. & supplements, 1982, Chapman
      & Hall.

*  When the assigned unknowns have been completed, the user is invited to do
   more group three unknowns (until they have all been completed).

*  A new user option can be selected which readies the support file for a new
   user and assigned three unknowns at random. A better way of doing this
   however is to use the supplementary program "newuser" which assigns
   unknowns to a new user on a more rational basis. Sets of three unknowns
   (with each compound being of a different class) can be given randomly
   to each user or a set of any number can be given manually. This program
   also reads the data from old user disks for later analysis.

*  Most of the support files are in ascii format and many of them can be
   changed (within limits) if required. Registered users will receive a
   program and additional information to aid changing the data files for the
   unknowns. In this way the various prerequisites and restrictions for each
   unknown can be altered if so desired.



---------------SECTION C -HARDWARE REQUIREMENTS & INSTALLATION---------------

At least EGA graphics with a colour monitor and 640K memory are required.

The program "setup" is supplied to install the "torganal" program and files.
Manual installation is possible and the following information should help.

As indicated above, information about the user is kept in the file user.txt.
For multiple users each user has to have his\her own user.txt file.

Modes of operation:-

Multiple users
    A.  Main files on hard disk (on multiple computers if required) and
        each user has their own floppy disk with their own user.txt file
        on it. (Recommended option.)

    B.  Each user has a floppy disk with all needed files on it.


Single user
    C.  All files on hard disk.

    D.  All files on a floppy disk.


Option  A.  (Multiple users, hard disk and floppy disks)

    Files should be copied to the subdirectory \torganal on the hard disk.

    Edit the file torganal.ini to indicate which floppy drive to use.

    Prepare floppy disks each with a user.txt file (use the program
    "newuser").

    To run the "torganal" program, first change the current
    directory to \torganal on the hard disk and then type torganal
    followed by enter.


Option B.  (Multiple users, floppy disks)

       Copy the main files to a floppy disk.

       Edit the file torganal.ini to indicate which floppy drive to use.

       Make multiple copies of this floppy disk.

       Use the program "newuser" to ensure that each disk has a different
       user.txt file on it.

       To run the "torganal" program, change the current directory to the
       floppy disk and then type torganal followed by enter.


Options C & D (Single user, hard disk or floppy disk)

       Copy the main files to a disk.

       Edit the file torganal.ini to indicate which disk (& directory) to use.

       To run the "torganal" program, change the current directory to where
       the torganal files are and then type torganal followed by enter.


Notes:
1.  Main files means

    torganal.exe    torganal.ini    mainmenu.txt    user.txt
    cclasses.txt    titles.txt      all the unk??.txt files

2.  It is recommended that the following files have restricted access:-

    setup.exe       torganal.doc     newuser.exe

3.  "Newuser", in addition to writing new user.txt files also reads the old
    user.txt file and stores (appends) some of the information in the file
    torgdata.txt for later analysis. It is therefore recommended that this
    program should be used on the same computer and directory each time. To
    prevent unauthorised access it has password protection.
         -------->  password is the word TASMAN  <--------



-------------------------SECTION D - Revision history------------------------
version 3.10
    first shareware version released in January, 1992.

version 3.11
    Minor changes made to support files only - released Feb, 1993.
    IUPAC name added if it was not already present for each unknown.
    Torganal.doc modified slightly to improve clarity.
    A few typographical and other errors were corrected in the
    unk??.txt files.


---------------------SECTION E - Registration and Payment--------------------

Torganal and the associated files are copyrighted work and are released under
the shareware concept. You may try out the program for a period of four
weeks; if you determine that it is useful and you wish to use it further you
must register and pay a fee.

This will entitle you to:-

      * a copy of the program which shows on the initial greeting screen
    that it is registered to your institution (institutional users
    only).

      * make multiple copies on multiple computers for student use at any
    one location (campus).

      * receive support from the author and additional files as outlined
    below.

ALL PROGRAMS AND DOCUMENTATION ARE SUPPLIED AS IS. NO WARRANTY OF ANY KIND IS

GIVEN AND THE AUTHOR SHALL NOT BE LIABLE FOR ANY DAMAGES OR LOSSES.

REGISTRATION FEES
For institutions with 1-50 users per year the once only fee is US$200.
For institutions with more than 50 users per year the once only fee is US$250.

To encourage direct use by individual students, the fee is US$20.

Payment is to be made to:-
    Dr Adrian J Blackman
    Chemistry Department
    University of Tasmania
    GPO Box 252C
    Hobart, Tasmania
    Australia 7001

On registration you will receive the following extras:-
    The program "userstat" which gives some statistics of usage (based
    on the file torgdata.txt which is written by "newuser").

    The program "unkedit" which makes it possible to edit the data files
    for the unknowns if you wish to do so.

    Unkslist.txt, an ascii text file containing the various names
    of each of the unknowns. In the files unk??.txt these names are
    encrypted so that users can't easily find out the compounds' identity.

    Titllist.txt (ascii text file) containing the titles of each test,
    measurement and derivative along with their identifying numbers
    which are needed if any editing of the unknowns is to be done.


A final plea:
    PLEASE REPORT ANY ERRORS AND SUGGESTIONS FOR IMPROVEMENTS TO
    THE AUTHOR AT THE ADDRESS GIVEN ABOVE OR E-MAIL TO:-

            [e-mail]