USE OF TECHNOLOGY FOR ORGANIC CHEMISTS
This laboratory is heavily dependent on, and inspired by, “Technology for the Organic
Chemist: Three Exploratory Modules” by Esteb, J.J.; McNulty, L.M.; Magers, J.;
Morgan, P.; and Wilson, A.M. J. Chem. Educ., 2010, 87, 1074 – 1077.
There are several technological tools available to organic chemists, and scientists in
general. These tools continue to change and evolve. It is important for scientists to be
aware of the resources available to them for up-to-date research, scientifically appropriate
databases, and professional presentation of scientific data. This laboratory will introduce
you to only some of the tools available to you. A lab period has been set aside as time to
complete this assignment. You are not required to complete this assignment during
laboratory time, but the instructor will be available during lab hours for questions.
Part 1: Research Tools
Online resources for the research scientist are invaluable, so long as the sources are
appropriate, reputable, and scientific. Websites from chemical supply companies, such as
www.sigmaaldrich.com, contain a great deal of information. You will be utilizing these
sources in various activities common to synthetic chemists.
EXPERIMENTAL PROCEDURE: Log into your chosen computer and open your
favorite web browser. Be sure to turn off the “pop-up blocker” in your browser as many
of the items you will be calling up show up in pop-up windows. Note the web browser
that you are using.
- The list of sites that you will use is available on the last page of this document.
In the past, ChemBioFinder.com was a great source of information for organic chemists.
Recently, however, much of the functionality of the site has been removed, except for
those who pay a fee to CambridgeSoft, the corporate entity running the site. As a result,
we will not use ChemBioFinder as a resource in this exercise.
Much of the same information that could be found on ChemBioFinder in the past can
now be found on wolframalpha. This is a “computational knowledge engine” that seeks
to deliver information on a topic, rather than present a listing of other web sites that may
be useful. Search for aspirin and record some of the information that you get.
Wolframalpha is a good site for a variety of uses. Type in today’s date and see what
information you can get. Play around with it a few minutes.
Change sites to the Sigma-Aldrich website. This is a website for a commercial vendor;
we buy much of our chemical inventory from Aldrich. Perform a search for aspirin. Go to
a page showing the structure of aspirin. There is much information available to you on
this page. What are some synonyms for aspirin? What is the CAS number? What is the
price of aspirin? To the left there is a link to the MSDS (Material Safety Data Sheet).
Click on this link Open with: Preview). Look through the MSDS, what is the LD50 (what
is this?) for a rat (choose any introduction method)? If the average rat weighs 250 g,
extrapolate the LD50 to the average human who weighs 68 kg. How many 325 mg
aspirin tablets would a sample of average humans have to take in order for 50% of them
to die? Look through the rest of the MSDS. Have you found anything else interesting?
Perform an Aldrich search on benzene. Find synonyms and the CAS number. Is there an
MSDS for this compound? If so, look through the MSDS for toxicity, LD50, chronic
exposure . information, etc. Have you found new terms such as lachrymator, tetratogen,
mutagen, air sensitive, moisture sensitive? Define any new terms you have found. If there
is an LD50, determine the lethal dose for 50% of humans if you scale up to the 68 kg
human mentioned above. Look up the MSDS for sodium chloride. Do you find anything
surprising about this chemical? Note anything that you learned in your notebook.
Go to the eMolecules site. (As an aside, this site started as Chmoogle, which seemed like
a clever name for a search site for chemicals. The lawyers at Google were not amused
and the name was soon changed to eMolecules.) eMolecules performs a number of useful
purposes for a chemist, including searching commercial sites to find vendors for different
chemicals. Search for aspirin. You will see the structure of aspirin, the molecular weight,
the ACD logP (what is this?) and two columns for Supplier and Supplier’s ID. Note that
some of the Supplier ID numbers are underlined. These are active links that will take you
to the supplier’s web site to get pricing information. Click on one other than Sigma
Aldrich. What is the price of aspirin from this supplier?
You will note that there are ways other than name to search in eMolecules. You can draw
the structure in the box using the tools provided. These tend to be problematic for some
reason. You can also add the CAS number in the search box. Another choice is to use the
“SMILES” method. SMILES stands for Simplified Molecular Input Line Entry
Specification. This is a “straight-line” method of writing complicated structures. We can
generate SMILES notation with ChemDraw. Open ChemDraw and draw aspirin. Select
(use the lasso button) the structure and then choose Edit > Copy as > SMILES. A
SMILES equivalent to aspirin has been generated and stored on the clipboard. While still
in ChemDraw, open a text box (the button with the “A” in it) and paste into the text box.
This is the SMILES version of aspirin. Try to make sense of the nomenclature and be
sure to write it in your notebook. Paste the SMILES name into the search box in
eMolecules and search. What is different about this result, compared to the search for
aspirin?
Change sites to the Patent Search site. The purpose for this site is obvious! Search for
aspirin among the patents. How many patents are listed? Pick one and read the
particulars. What is the purpose behind the patent? Who is listed as the inventor? Who is
the assignee? What is the application date? What is the patent number? (This is an adsupported site so you will have to navigate past the advertisements to find all of the
information.) Repeat this exercise for your assigned compound.
The last online resource we will utilize is the Spectral Database for Organic Compounds
(SDBS) maintained by the National Institute of Advanced Industrial Science and
Technology (AIST), Japan. The National Institutes of Health, National Institute for
Standards and Technology, National Science Foundation, etc. in the US all maintain
databases as well. However, the SDBS is particularly useful for organic molecules. Go to
the SDBS site, agree to the disclaimer and enter the website. On this website, you can
obtain a wide variety of spectral information about organic molecules (this will be
especially useful in CHEM 242!).
Do a search for aspirin. Then, type in the molecular formula for aspirin in the molecular
formula box on the screen. Be sure that you are using the letter O and not zeros for
oxygen! How many structural isomers are there for this molecular formula? Pick one
structure that is not aspirin. Note the SDBS number, the compound name, draw the
structure, and note the spectral information (listed under “spectral code” to the left – you
may not know what these mean yet, that is okay) which is available. Do you now see why
searching by molecular formula could be problematic?
Perform another search in SDBS using another molecular formula. (Use 6-10 carbons,
8-14 hyrogens, and 1-3 oxygens.) Note the formula you used, the number of structural
isomers you found using this molecular formula. Choose one, draw the structure, give the
SDBS number, compound name, and any spectral information for this compound.
Part 2: Database Tools
Online databases provide more research-oriented information than the online research
tools that you have looked at so far. Databases can be used to search for information on a
scientific topic from general to specific. Often, researchers perform online searches in
their specific research areas to determine previous work in the area, as well as investigate
current publications that may provide useful information. You will be looking at
databases that are available through the Dickinson College LIS site.
EXPERIMENTAL PROCEDURE: Log into your chosen computer and open your
favorite web browser. Be sure that “pop-up blocker” is disabled as it was in Part 1. Note
the web browser that you are using.
Go to the Waidner-Spahr Library Databases website. The databases are listed in the
subject cloud by subject area, click on the Science link. Click on the Pubmed link.
Pubmed is a free database of biomedical and life science journal articles. The service is
run by the United States National Library of Medicine and the National Institutes of
Health. At the search page, type in “aspirin.” How many research articles on aspirin did
you retrieve? Narrow your search by typing aspirin with some other modifier. A modifier
can be any related word to your target (examples: aspirin synthesis; aspirin uses; aspirin
history; etc.). What modifier did you choose? Why? How many articles did you retrieve
this time? Click on one title link and look at the abstract. Note the reference that you have
chosen in your notebook. Are you interested in this article? Articles with the greenstriped papers icon are free for download, those without may charge for the service.
Return to the list of science databases. Click on the Web of Science link. Web of Science
is a database of more than 8000 science journals, with extensive tagging. Do a search for
aspirin. Did you get more or fewer articles? Refine the search by narrowing it down to a
particular subject area by clicking the “more options” tag under Subject Areas to the left.
These can be arranged alphabetically, search for articles under the “Chemistry, Organic”
subject heading. (If there are none, choose something similar.) How many articles do you
get now? What is the most recent article? What is the most “relevant” article? Articles
can be accessed by clicking the “Get It!” button. Try this and see the result.
Return to the list of science databases and click on the Science Direct Link. Science
Direct contains nearly 10 million articles from over 2500 journals and thousands of
reference works and is operated by the publisher Elsevier. Note that the search (for
aspirin) can be refined by checking content type, title, topic, or year. Titles available in
full text are indicated by a green icon. Narrow the search to a publication in a journal in
2009 or 2010. This gives you a quick way to limit your searches. Record the reference,
using ACS style citation.
The last database is the American Chemical Society (ACS) publications database. The
webpage for any ACS journal will have links to their database, so we will enter through
the ACS publications homepage. In the upper right hand corner is the search for all ACS
journals. Type in“aspirin” in the subject box, choose “anywhere” from the pull-down
menu, and hit search. How many articles did you find? Choose one, note the reference,
and click on the PDF of the article. Summarize the information in a sentence or two.
Dickinson has subscriptions to all ACS journals so any journal article you find is
available.
Information Site URLs:
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7.
American Chemical Society Publications: (http://pubs.acs.org/)
ChemBioFinder: (http://www.cambridgesoft.com/databases/login/?serviceid=128)
Waidner-Spahr Library: (http://lis.dickinson.edu/Library/LISDatabases/index.cfm)
eMolecules: (www.emolecules.com)
Online SMILES Translator: (http://cactus.nci.nih.gov/services/translate/)
Patent Search: (www.freepatentsonline.com)
Structural Database (SDBS): (http://riodb01.ibase.aist.go.jp/sdbs/cgibin/cre_index.cgi?lang=eng)
8. Sigma-Aldrich: (www.sigmaaldrich.com)
9. Wolframalpha: (www.wolframalpha.com)