The Literature of Chemistry – SciFinder Scholar
Organic Chemistry Laboratory
The literature of chemistry is massive beyond imagination. Millions of articles in tens of thousands of journals have been published with information relating to the field. To manage this unwieldy resource, the Chemical Abstracts Service (CAS) has designed a tool called SciFinder that is designed to allow easy searching of the articles, combined with a brief abstract and other relevant data.
In this “information resource” lab you will learn to use the tool as a way to find authoritative answers to questions of a chemical nature. There are some limitations to using this tool, however. SciFinder is a very heavily used professional resource. It’s not Google and it’s not a web browser. The data in the CAS repository is immensely more valuable than that which comes from an online search. Consequently, CAS charges a very high price for schools wishing to use the service. To make costs more manageable, small schools usually purchase access to SciFinder on a shared basis. This means that only a certain number of users at the sharing schools can access SciFinder at any given time. You may find that it is not available at the moment that you first attempt to use it. Also, you cannot launch SciFinder from your computer. At this writing, SciFinder is available on the computers in the reference area in the Jenks Library. Additionally, students working on extensive research projects may install SciFinder on their own computers.
Getting started with SciFinder
SciFinder use always begins with an information problem that needs to be solved. Examples of these problems are…
• Has anyone ever studied the toxic effects of biodiesel on plants?
• Does anyone sell the chemical I need to use in my research?
• What are the properties of the reagent I’m about to use?
As a specific example, suppose we wish to synthesize 2,15-dimethylhexadecane, one of the components of the tse-tse fly mating pheromone. If we use our normal restriction, organic starting materials with less no more than six carbons, two approaches emerge, using a difunctional central molecule to which two side groups that could be attached. Those methods are:
Task #1 – Exploration of Chemical Structures
Notice! The instructions below are not in a step-by-step tutorial form. Since this is a lab assignment, you are expected to be experimental in your approach. Please use your notebook to keep good records of what you do, especially if you “figure out” how to do something that wasn’t obvious to you. Note that the images on the screen were from the Macintosh version of the program; the screen shots that you see will differ if you are using a PC-compatible version.
Click “OK” to get past the rather annoying “Message of the Day” window, then go into “Explore” mode. Click “Chemical Structure” then draw the structure of a molecule using the icon based tools in the window.
Experiment for a little bit and you’ll have no problems. Ask a TA or your instructor if you can’t figure out what to click. But first, try things. You won’t hurt anything. For example:
After you have become familiar with the controls, draw the diyne from the previous page, click “Get Substances” then wait patiently. Normally, the most relevant reference is the last one of the list (go figure!). Scroll all the way down and notice that the last one has the most references (306 as of this writing).
Click the little microscope icon to the left of the Registry number to read details about this molecule. Record the following in your lab notebook:
CA Index name
Boiling Point (click on “Experimental Properties”)
Click to view the Infrared Spectrum of the molecule. Close the windows you have caused to open and return to the window that has the microscope icon.
You would click on the first icon (References) if you wanted to learn about the use of or production of this molecule in primary journals from the scientific literature. Instead, click on the second icon (Commercial Sources) to learn how many suppliers are available for this molecule.
Repeat for the other three molecules of interest above. Note that “Experimental Properties” may not be available for all of the molecules, but you can still estimate many of them with the “Calculated Properties” that are provided.
[pic] Details icon [pic] References icon
[pic] Commercial Sources icon [pic] Regulatory Information icon
After locating two starting materials that you consider to be available, do a web search for the safety risks associated with the materials. There are many ways to do this. A good resource is ChemExper online which is at
Note that SciFinder also provides regulatory information with the same sorts of information, but it can sometimes be easier to interpret the data from ChemExper. It is easiest to use the ChemExper site if you can search by CAS number. In the “Enter a name, molecular formula or cas number” field, enter the CAS number for one of your molecules, then click “Search”.
On the right side of the output screen, notice the Hazard/Risk/Safety entries. These codes are standard codes used by the European Union to label hazardous materials. Allow your mouse to hover over one of the codes and it will reveal the meaning of the code. Alternately, you might wish to put together a list of the codes to keep in a handy place in your lab notebook. You can find the information at:
Task #2 – Locating a Chemical Substance
Remember searching for your Take Two molecules? You used the web and you finally found a source for the information you needed. Some of you found that information quickly, for others it was more difficult. SciFinder is the far better way to search for such data.
Click the “New Task” icon at the upper left corner of the main window.
Click “OK” to indicate that you wish to discard your prior task and move on to something new.
Locate | “Substance Identifier”
Enter: atorvastatin in the “Enter Substance Identifiers” text box, then click “OK”
Wow. There are a lot of references! (3805 when I checked on 11/15/2008)
Click the “References icon”
For this substance, retrieve “References associated with” the “Preparation” of the molecule. OK!
That’s better. Not so many. (121)
Remove Duplicates (none)
Refine | Document Type | Patent | OK
Scroll all the way to the bottom and you will see, in the earliest reference, the name of the person who first received a patent for atorvastatin (Lipitor). He’s a fairly famous chemist these days.
Now, do the same for your take-two drugs. Find out who first received a patent for each of the two Take-Two drugs you worked on. What year was the patent issued and in what nation?
Task #3 – Researching a topic
This is key to any research project. You begin by finding out “who knows what?” about the topic you are interested to study.
Click the “New Task” icon.
Explore | “Research Topic”
I wonder if biodiesel can be made from corn. I wonder if it’s toxic. Hmm… I am interested in: biodiesel corn toxicity (OK!)
Wow. There are articles about this. How many? Get the references. Remove duplicates. How many are there? Click the “Detail” icon and skim the abstract. If it interests you, print the page.
Did it interest anyone else? See how many people have cited this paper in their own work by clicking “Get Related…” and then “Citing References”.
Task #4 – Author Search
In this portion of today’s lab you will do an actual research project. The question: What members of the Green Chemistry education community are publishing about biodiesel or toxicity? We honestly don’t know but we would like to. Go to the google map found at:
and select the name of two participants: one from North America and one from outside North America. After you choose your chemists, write down their names and affiliation info using the map display. Next create a bibliography of each author’s professional publications by using the Author Search in SciFinder.
Click “New Task”
Explore | “Author Name”
Enter one of the names on your list
Wait patiently then use the checkboxes to select the appropriate names. For example, when I entered the name of my colleague, Denyce Wicht, I received this result:
Her name was not in the database as I entered it, but her name (along with her middle initial or middle name is in the database). I would then click both of those boxes and “Get References”,giving me a screen with bibliographic references to all of the papers authored by this person.
Note that if there were several people with that name (there’s more than one chemist named Irvin J Levy, for example) you will have to make an educated guess about the relevance of a given reference.
For each of your chemists, search for the articles that were authored by that individual and prepare a report of the bibliographic information for each of them.
Something unclear? Try: www.cas.org/SCIFINDER/SCHOLAR/resources.html
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