Electronic Notebooks
You will have to
prepare a report of what you find. By opening a program such as Claris
Works and cutting/pasting various graphic images, you can prepare a
professional looking report "on-the-fly" as you acquire information.
To copy any image present in a Netscape
browser, point the mouse cursor over the image and hold the mouse button down
until a menu appears. Select copy to "copy this image", then move to the Claris
window and paste the image using the item in the edit window. Text can be similarly
captured. DO NOT attempt to start Claris on a Silicon Graphics workstation or
a PC system: this program is not available on these systems in the department.
The World-Wide Web ("Web") is a global
information system created by
the British scientist Tim Berners-Lee. It enables
access to text, images, animations, sounds, "hyperactive" molecules,
and databases. This experiment is itself choreographed using the Web mechanism.
Click on the question mark at the left to visit the
"center of the Web". Note that during "peak" times of day access to the USA
may be sluggish. There are other collections of more focused chemical Web
collections, such as "Global Instructional Chemistry"
Hotbot is one of a series of
"Indexing Robots" that trawl the Web indexing it. The default options presented
can be augmented by "expert" mode. Use this system to see what sort of
information is retrieved on Penicillin.
The Bath
Information Delivery System is an on line version of the science citation index,
in which all primary papers published in essentially all the important chemical
journals are indexed by subject, author, date and several other fields. By default,
the search will start in the current year, e.g 1996, and currently goes back to 1981.
A typical keyword search will produce similar information as the other major on-line
chemical information service CAS ONLINE, with the significant difference that the
BIDS system is free to individuals in the College.
In this part, you should (a) perform a keyword search relevant to your (putative)
dissertation topic, and (b) develop a set of suitable keywords for finding
relevant information about the penicillin to cephalosporin conversion performed in
technique 2. The user name and password required for doing this are available from
course demonstrators.
CAS On-line is the primary source of
abstracted information on Chemistry. Some 14 million chemicals and 15 million
records are contained on this database. There are three principal access mechanisms
to CAS; a) a simple terminal based interface where commands are typed from the
keyboard, b) A structure drawing interface called STN Express and c) a more
complete information organising environment called SciFinder. Because CAS operates
on a commercial basis, and the costs of using it can be very high, we will illustrate
its use via method a), using small demonstration databases.
Silver Platter gives on-line access via the World-Wide
Web to "samplers" of a number of more medically orientated databases (the full
versions are available via a system called MacSPIRS, but there is no need to
use this here). Select MEDLINE and find out any
relevant references to penicillin. Are there any other useful databases?
Libertas: The College Libraries on-line
catalogues. Interaction with either bulletin boards or information gleaned
from say e-mail may lead to promising books or journals that you might wish to
consult in the conventional printed form. You can quickly find out if this
material is available in either the central College or departmental libraries
by logging into the Libertas system. If it is, you can even reserve the
material in your session. For this search, you should determine whether any
college library has any books on penicillin, identifying
any candidates likely to be useful for the synthesis of such
molecules.
Aldrich: Chemical Availability
Before starting experiments, it is normally necessary to identify
commercial sources of any reagents you may be using. The Aldrich is one
on-line catalogue enables you to do this easily. In this case, you should look for penicillamine
in their database (What happens if you enter Penicillin?).
Fisher Scientific: Health and Safety Information
You can also acquire the relevant health and
safety information. In this case, you should look for in the catalogues of
another chemical supplier Fisher for MSDS safety sheet for any penicillin
in their database (The Aldrich MSDS information is only available on a commercial
basis).
Daylight Information Systems: The World Drug Index.
Some chemical information companies make available on-line sub-sets
of some of their databases. Daylight Information systems has
pioneered innovative interfaces to such information. Here you can
search the World Drug Index (WDI) for any information on
penicillin. The results of this search are used to generate
a so-called SMILES descriptor of any hits, which can in turn be
used to search a current literature database called Savant. This
can be used to generate synthetic methods for preparing compounds
identical with, or similar to your search query. If you are really
ambitious, try the "Grins" interface to structure building rather than
using the SMILES string.
The Cambridge Chemical Database Centre.
Whilst keywords based on the title of a paper or its authors may provide some
useful information, this will not necessarily produce information about an
individual chemical compound. Here the search must be defined by actually
drawing the compound of interest, or even merely a "sub-structure" and then
performing a systematic search based on this criterion rather than one based on
text. This requires more specialised programs, and also as it happens a great
deal more computer time. Here you will perform a sub-structure search for the
penicillin ring system on a database containing the 3D coordinates derived from
crystal structure solutions.
The Brookhaven Database at the NIH
or the European Bioinformatics Institute (alternative Site).
This database contains all known protein and macromolecule crystal and NMR
derived structures. A number of enzymes are known to act specifically
on penicillins, either to digest them or to form them. You should use this
database to find out whether any enzymes with "penicillin" are known, and what
their 3D structures might be.
The Swiss-Prot Sequence Database at the University
of Geneva
contains information on the primary sequence structure of bio-polymeric
molecules. You should use this
database to find out whether what the sequence of any
enzymes associated with "penicillin" are.
The Beilstein Crossfire System.
Here you will perform a search for
penicillin on a database containing specific property information about
the compound, the Beilstein database. You should try to find out melting points
of any compounds identified.
Local Database Creation using ChemOffice.
This technique will also illustrate how information produced
by a search, in this case the crystallographic
co-ordinates, can be transferred from the computer where
the search was conducted to a local Macintosh system, using
the "ftp" file transfer method Here it is entered into the
equivalent of a "molecular spreadsheet" called ChemFinder,
in which various operations which help to visualise the
data are performed. Other data relevant to the compound can
be entered directly from your own laboratory observations,
and the entire collection of data constitutes your own
local database of information.
Chemical Reaction Accessing using ISIS/Base
Sometimes even information about a specific compound is too
general to be useful. Much of chemistry is about the
chemical transformation of one compound into another,
whether it can be done at all or in good yield, what the
reagents and conditions are etc. Such a search implies a
quite subtle relationship between two or more compounds.
Again, specialised software is needed for this task. You
will be using a system called ISIS/Base. Here the end
results of a search is not so much a file containing
information about one compound, but one or more pages of
information relating to the chemical transformation,
including the literature citation.
VChemLib and
Molecules-of-the-Month
are two current awareness local databases containing organised "stories" about specific molecules.
Anyone writing an exemplary report on Penicilins could find themselves contributing to
these databases!
Electronic Conferences.
Start your search by
visiting the ECTOC and
ECHET96
electronic conferences. These were the first electronic conferences with
organic chemistry as a general theme, and both support keyword
searchs. You should find out if penicillins were discussed.
Electronic Journals.
Increasingly, journals are starting to appear in electronic and searchable
form. Start your search by
visiting Chemical Communications.