MEDICINAL PLANTS

“Poisoning is not a matter of chemicals, it is a matter of dose size.”
Paracelsus

I found this list of medicinal plants while "gardening" on the web. There should be some interesting chemistry and biology associated with these. Each student will select one of the plants and write a report about it. Completing all parts of the assignment will involve information searching and retrieval from the web and electronic sources, drawing in ChemSketch, and continuing development of a web site.

Part I

Begin by choosing one of the plants listed. Send an e-mail to me with the Subject line plant X, where X is the name of your plant. As each plant is selected by one of you, I will put an X next to it in the list and it will no longer be available to anyone else. (Each time you view this page, press Reload or Refresh so you will see the new X’s.) If I do not reply to your message, it means you have your first choice.

Searching
There are two main categories of information-searching you are learning in this course: general WWW searching and, more specifically, electronic sources of science information (both library and internet based). For both, you will learn how to formulate search stategies. You can begin searching for your plant on the web immediately. As you learn more about other scientific electronic information sources, these will be added to the assignment in Part II.

Find answers to these questions using website sources (not journal articles):

• What are the plant's common and botanical names (remember to put the latter in italics)? In what parts of the world is the plant found? What are some other aspects of its cultivation/environment? Is it considered endangered or invasive?


• Find an image of the plant to incorporate in your page and request permission to use it. Give credit to the source of the image and its copyright holder. Do not link to the outside image; save it to your account.


• What are the pharmacological effects of the plant (e.g. anti-inflammatory, vasodilatory, antimicrobial, anticonvulsant, sedative, antipyretic, etc.)? Are there any adverse effects?


• What is the effective agent in the plant? How is the effective agent administered? In what part(s) of the plant is it produced? Is there more than one effective agent?
  
  
• What is the chemical structure of the effective agent(s)? Try to find a drawing of the structure. Give all known common and systematic names for thecompound(s).
  
  
• Other interesting facts and figures.
  

While you conduct the search, keep a Search Log (as a document file in Word). In the same way that you write down what you did, what you observed, what your results are in your laboratory notebook, you should do the same thing in a search log. It is a record of how you conducted your search.

Suppose this search was really important to you or your employer, and that from time to time you would add to it, or be asked questions about it. After reviewing your search log, you would be able to continue your search without repeating old ones, and be able to answer questions about what you have done. The log should note not only the search terms you used and the number of hits you get from a search, but also contain the specific references you find that are relevant to the search. See the example in the link above. Much of this text can be constructed by copying and pasting URL's and brief information from your search sites.

Expect to cite at least 10 different sources from general web searching (no dictionaries or encyclopedias). Your citations should be primarily from "trusted" sources from domains such as edu and gov, for example. Information from a blog, written by someone you have no knowledge of, should be avoided. Likewise, look carefully at any information contained in a commericial site (.com) that is offering something for sale.

Project Format is an HTML document named plant.htm that is accessed by a descriptive link on your web site CHEM 350 Project Page. (Remember, the Project Page will eventually link all your web projects in this course and it is in a project directory below the public_html directory.) The plant report document and any associated files should be in a directory, plant, under the project directory which is a subdirectory of your public_html directory.

The length of the report, exclusive of images, on the web page should be equivalent to several printed pages. This means primarily that your report should be of sufficient length to answer the questions posed completely. Please use complete sentences; many sentences per paragraph; and many paragraphs.

A reader should have the impression that the subject matter was written by you and not copied (plagiarized) or cobbled together from various sources. Don't overuse images, but a judicious choice of them will enhance your presentation. When using terms such as "expectorant" or "carminative" or other such words that are not commonly used in chemistry, make sure you define them. If, for some reason, you cannot answer a question, state what you are not answering.

Do not merely fill in the blanks -- use complete sentences for all parts of the report. Do not use a "question and answer" format. If you can't find the answer to one of the questions, explicitly state so, and in the search log specify how you searched to find the answer. Please organize the sections in a logical, progressive manner and write with enthusiasm!

• Use the H1 tag for your report title.
• Report title should appear in browser bar.
  
• Put your name near the top of the page.
  
• Include a Table of Contents (unordered list) pointing to an introduction, various sections of the report, and the bibliography. Use the Named Anchor HTML tag to link from the TOC to the sections.
  
• Use the H2 tag for section titles.
  
• Within the body of the report, for each reference use a number enclosed in brackets (e.g., [12] ) that is hyperlinked to the appropriate reference citation at the end of the report in the Bibliography section (Named Anchor, again).
  
• For all citations of web sites, hyperlink the reference citation in your bibliograpy section to the site. See the citation style page in the Manual.
  
• Use tables, text wrapping around images, etc. to control the layout of your document.
  
• Link to your search log at the end of the web page, below the bibliography.
  
  

  DO NOT compose the report in MS Word and convert it to a web page. Do not use styles or CSS.

Remember, a pleasing presentation is an important aspect of web pages -- your project should not look like a printout of straight text on a blank page or a page with pictures between large blocks of text (or worse: big pictures and not much text). Control the space on the page. Even if not specifically required above, try to use as many HTML mark-up tags as possible.

Submitting the Medicinal Plant I project assignment on the Web

Your project should be readily accessible on your web site. If you haven’t already done so, please organize your site according to the guidelines given earlier. Specifically, on your front page there should be a link, “CHEM 350 Projects”, that opens a page in a projects directory. On this page should be a descriptive link to the report in the plant subdirectory.

By now, either as another part of your site, or as part of this project, you will have requested permission to use a copyrighted image. You don't have to send me copies of your correspondence but be sure to give credit for all your images as you did for the development of your web page. If the image is free to use, then give credit to your source.

Please check that you have fulfilled all the requirements set out for this project. If you have any problems or questions, you should let me know sufficiently far ahead of time that I can help you.

Submit the files in your plant subdirectory to WebCT as a zip file. All dependent files must be viewable from the plant.htm page in WebCT!

Turn in print copies of the web page document (printed from the browser page with the URL left-justified in the footer) and the search log.

Press Reload/Refresh to see the latest X's.

Medicinal Plant List

Part II

A. More Searching

You have done some web searching for information on your active compound. You should now do an even more methodical search for specific chemical information from journal literature sources particularly the structure, isolation, characterization and laboratory synthesis of the compound(s). (If the compound has not been synthesized, but has been derivatized, cite the derivative's synthesis instead.) (Characterization -- describes characteristics of the compound such as m.pt./b.pt., ref. index, NMR and IR, etc. )

Search in Scifinder Scholar and these publishers' journal databases: ACS, Elsevier (Science Direct), Plant Science and PubChem. [Note: you can turn on a Search History in Elsevier and save it.] Be sure that you are searching all years available in the database. Your goal is to find at least two full-text articles reporting the information specified in bold above. You can search sources beyond those specified above, but those are a basic requirement and most likely to be productive.

While you conduct the search, continue to keep a detailed Search Log. The search should continue underneath the general web search in Part I, that is, there is only one comprehensive and on-going search log that is linked at the bottom of your web page. Here is an additional example search-log-2.doc.

Incorporate this new information and references into your Medicinal Plant web page into a new section titled Isolation and Synthesis. The new section should be added to the TOC and linked with a named anchor. All new references to journal articles should have a bracketed reference number that is hyperlinked with a named anchor to the corresponding number in the Bibliography section. In your Bibliography section, be sure you pay attention to the requirements for linking journals . See the citation style page in the Manual.

Please do not leave the impression that you have not searched thoroughly for the information. If you are having trouble, you should see me. At the due date, it is too late to say that you couldn't find anything.

(If your compound is well-known and easy to find, you should compile a comprehensive list of journal sources, including both the first known isolation and the latest, as well as various syntheses.) Incorporate the information you found in your web page report.

Print the abstracts of two of the most relevant articles from any of the databases (not from the article itself). Now, access one full-text article and print the abstract directly from the article (the abstract should be different from the previous two). Be sure you understand the difference between accessing the abstract of an article from an online database and accessing the article itself (and thus the abstract that is included).

B. Structure

Now that you have found the structure of the active compound in your chosen plant, use ChemSketch to draw it. If there are oxygens, nitrogens or sulfur atoms, explicitly show the non-bonding electron pairs. If there are stereocenters in the molecule, you should make every effort to find a structure that specifies the stereochemistry. Use wedge and dashed lines at stereocenters, where applicable. DO NOT perform a 3D optimization while in the sketch pad.

Resize the structure for presentation on your web page. Export the drawing in the gif format and insert it in your web page with an appropriate caption. Provide an image border. Be sure the image is not distorted on the web page.

In ChemSketch, copy the 2D drawing to the 3D viewer. Optimize the structure in 3D. Render it as ball-and-stick. Use these atom colors (here and always): H = white; C = black or gray (or cyan); N = blue; O = red; S = yellow; halogen = green.

Rotate the structure for a good 3D perspective. Choose a background color that is compatible with your web page. You can use the zoom tool to resize the molecule.

To make a jpg file of your 3D molecule, save the file as a bitmap (.bmp). Open the bmp file in Paint (or similar program). Save the file in the jpg format. [Question: why is the ChemSketch drawing saved in the gif format and the 3D rendering in the jpg format?]

Place the 3D structure in your web page with an appropriate caption.

Print the 2D structure from ChemSketch to turn in.

Save your ChemSketch files to turn in to WebCT (one each from the drawing program [.sk2] and the 3D program [.s3d]) and the gif and jpg files.

Submitting Part II

Submit the plant project web page and all subsidiary files as a zipped file to WebCT. Include the ChemSketch and graphics files in the zip file. Turn in the printouts of the web page, the article abstracts, graphics and search log.