Organic Web Sites

A lot of web sites in organic chemistry use a piece of software called Chemscape Chime, from Molecular Design Limited (MDLI), the makers of ISISDraw. This software allows certain files containing 3-D information on molecules to be manipulated by the viewer - rotated, zoomed and changed from stick to space-filling models. Most of these sites contain links to permit downloading of Chemscape Chime from its manufacturer, MDLI; it resides in Netscape quite invisibly so long as you have version 3.01 or higher. Once you have downloaded it, there are several sites with tutorials on how to use it effectively, e.g. at UMass, Dublin City University, Cabrillo College. Chime rotates molecules with the left mouse button ("shift" right and left give others); the right button gives a menu which allows you to select space-filling, ball-and-stick and other colors.
You may also want to download a free copy of ISIS Draw itself, the software I use to prepare exams and enrichment materials for you; it interfaces nicely with word processors and can pretty up lab reports nicely. With the latest free download, there is an accompanying nomenclature program. I have prepared a short set of instructions for ISIS Draw. If you want to make organic structures for a web page I recommend ChemWeb; it isn't as convenient a drawing program as ISIS but it has the .gif output needed for HTML.

General Chemistry Review Nomenclature and Stereochemistry Organic Reactions and Synthesis Reaction Mechanisms
Sample Exams and Problem Sets Applications, Enrichment Spectroscopy Lab Safety

Check out Web-sters' Organic Chemistry for links to lots of other sites with information on just about anything about Organic Chemistry that students would be interested in. Professionals might want to try World-Wide Organic Resources.

General Chemistry Review

Ms. Liina Ladon, Towson University Chemistry Tutoring Center: lots of tips on calculations and other tough stuff from general chemistry.

David Wilner has a whole summary of a general chemistry course on line, starting with a section on "how to learn".

Jamie Bishop, Bon Shih and Abidemi Adeboji: an on-line textbook, chatroom, laboratory, etc. This site seems to have vanished -- it may have been a student-created site.

Dr. Paul Young at the University of Illinois, Chicago, has a review and problems on structure and bonding.

Nomenclature and Stereochemistry

Dr. Dave Woodcock, Okanagan University College: rules for nomenclature (IUPAC, R/S/E/Z); requires downloading Chemscape Chime for stereochemistry part (at the end of the nomenclature). Interactive. An excellent site, but you will have to page down before you can make a choice on the nomenclature tutorials.

The actual IUPAC rules (not including stereochemistry) have been put on the WWW by ACD labs. More than you ever wanted to know about nomenclature.

The official IUPAC Basic Terminology of Stereochemistry, with instructions for drawing compounds in three dimensions.

California State University, Dominguez Hills: graded R and S nomenclature problems using Fischer projections. Interactive. I found this helpful, but hard to get out of. Now it seems to be defunct.

Dr. Linda Sweeting, Towson University, instructions for using ISIS Draw

Dr. Donald Pavia, Western Washington University: pictures of molecules which can be rotated for viewing; requires downloading Chemscape Chime from MDLI, the makes of ISIS. Interactive. Instructions for Chime.

Dr. A. C. Pratt, Dublin City Univerisity: conformational analysis tutorial; requires downloading Chemscape Chime and has an excellent short tutorial on how to use Chime effectively to rotate the structure and view different modelling styles. Interactive.

Dr. Lev Ryzhkov's stereochemistry summary.

Ms. Liina Ladon's helpful tips on bonding, nomenclature, stereochemistry, and problem-solving strategies.

University of Wisconsin's multiple choice questions called ConcepTests; select organic or other chemistry course and the topic of interest.

Brunel University's definitions of organic chemistry terms, in alphabetical order, searchable only using your browser. I would have liked internal links, e.g. from acid to Lewis acid. Also, multiple choice exam banks and a link to IUPAC for nomenclature.

Dr. Paul Young of University of Illinois at Chicago has his whole course on line, including stereochemistry.

Colby College has some definitions, samples and problems for stereochemistry, plus some shockwave movies.

Stereochemistry tutorials from Drs. Abby Parrill and Jacquelyn Gervay at the University of Arizona

Dr. Karol Bruzik at the University of Illinois, Chicago, reviews stereochemistry for pharmacy students.

The Regis company sells chromatography columns to separate enantiomers and has a pdf Review of Stereochemistry.

Organic Reactions and Synthesis

Dr. Linda Sweeting, Towson University: reaction summaries and quizes for all reactions, with text references to Schmid. Interactive quizzes for all reactions.

Dr. Linda Bush, Salisbury State University: course outlines, exams, and flashcard quizes for Organic 1 and Organic 2. Interactive. This site seems to have changed URL's and not provided a new link from SSU Chemistry. Let me know if you find it.

Dr. Todd Lowary and Dr. Christopher Hadad, Ohio State University: reaction drill "flashcards". Interactive. Much Like Dr. Sweeting's but one reaction at a time.

Dr. Abby Parrill, Michigan State University: lots of good stuff including quizzes and animations. Interactive.

University of Wisconsin's multiple choice ConcepTests.

Julie Donan, student at the University of Kentucky: Course outline with links to tutorials, many at other universities. LIke many student sites, this one seems to have been short-lived.

Drs. Lev Ryzhkov and Dr. Alan S. Wingrove, summary of all several different sets of reactions, including interconversions of Organic Chemistry I on one page and details of SN2, E2, SN1, and E1 competitions.

Dr. Paul Young of University of Illinois at Chicago has his whole course on line, including functional group reactions and comments on mechanisms and intermediates.

Reaction Mechanisms

Dr. Brent Iverson, University of Texas, Austin: movies of reaction mechanisms made using space-filling models, from quantum mechanical calculations. Select UT Virtual Campus for Chime. This is really cool! He seems to have tucked the movies away and I could not reach him by the emali link. Let me know if you find them.

Savage, Fleming and Hart of Brigham Young University: movies of reaction mechanisms with orbitals. Some options show the changes in the highest occupied molecular orbital (HOMO) and others the lowest unoccupied (empty) molecular orbital (LUMO). Only samples are available since they are selling the movies on CD-ROM. Requires yet another plug-in.

Student generated study guides at Pennsylvania State University Schuykill Campus, instructor Dr. T. H. Eberlein. Nothing fancy but you may find them useful.

Dr. R. Ehrler of Germany: this collection of movies of reaction mechanisms and stereochemistry may require download of the SGI Cosmoplayer to view the VRML files.

Sample Exams and Problem Sets

Dr. Linda Sweeting, Towson University: reaction summaries and quizes for all reactions, with text references. Interactive.

Dr. Linda Bush, Salisbury State University: course outlines, exams, and flashcard quizes for Organic 1 and Organic 2. Interactive. Check this out! Sorry - URL has changed and there is no link to it from the Department.

Dr. Todd Lowary and Dr. Christopher Hadad, Ohio State University, syllabi, problem sets, exams, lecture notes and flashcards. Interactive. Check this out!

University of Pittsburgh has a variety of things for the organic chemistry student.

Dr. Craig Fryhle and the PLU, Pacific Lutheran University: syllabi with learning goals for organic chemistry (like my study guide in words) and links to some other pages. The molecular model kit has some nice stuff, mostly for enrichment.

Applications, Enrichment Materials, Study Tips, etc.

Polymer Macrogalleria

Dr Sweeting's Enrichment Handouts

Biochemistry and biology information -- practically an intro course in biology.

Spectroscopy

Basic introduction to the electromagnetic spectrum from NASA.

Dr. Paul Young, University of Illinois at Chicago, IR, MS and NMR Tutorials with solved problems, allowing you to choose what help you need. Note that there are spectra for 10 different compounds in each section.

Virtual Mass Spectrometry Laboratory from Dr. Joe Grabowski at Pittsburg. In progress

Dr. Brian Tissue at VPI&SU: NMR basics summary

This link to Wiley's SpectroscopyNOW NMR site also gives you access to MS, IR, UV and more. There is so much information on this site, it is hard to find the educational stuff. Look for on-line books.

Lectures on NMR spectroscopy from Imperial College, London, Dr. Henry Rzepa, which include some practucal information about obtaining a spectrum as well as chemical shift and coupling constant information.

Dr. Craig Merlic and Mr. Barry Fam (and Dr. Jane Strouse) of UCLA have problems using NMR (intengrated proton and/or carbon) and IR spectra which are displayed on the screen and can be expanded. The solution is available -- but don't look it up until you have struggled with it a while. I recommend the zoom feature which allows you to select a region. There is also a file of IR spectra for comparison of functional groups.

Dr. Craig King and Mr. Yue-Ling Wong have a summary of NMR principles, sample spectra and some problems (needs a plug-in).

Arizona State University NMR site with links. The lecture notes on NMR in MCB598 are hand-written and have little text connecting the equations and drawings.

Advertising demo for IR Tutor show what we have available in our Learning Center.

Thermo Galactic Spectra OnLine provides the MS, IR, UV, Raman, etc. spectra of compounds by name (or partial name), formula, molecular weight and even absorption characteristics.

In the NIST Chemistry Webbook you can search by name (or partial name), formula, etc to find infrared, mass, ultraviolet and thermochemical data on a wide variety of organic compounds. Vapor phase IR spectra look quite different from solution, pure liquid or solid phase as there are no molecular interactions such as hydrogen bonds; solution phase spectra may have solvent peaks, in spite of standard methods to subtract or compensate. You may need to download a plug-in.

Lab Safety

Towson University's own rules for the organic chemistry lab: SAFETY AND LABORATORY RULES for ORGANIC CHEMISTRY LABORATORIES and STANDARD OPERATING PROCEDURES IN THE ORGANIC CHEMISTRY LABORATORY

Towson University's overall rules for safety in the chemistry lab and elsewhere on campus are available at the web site for Environmental Health and Safety. These are the rules from which ours derive, and are far broader in scope. It even includes lists of chemicals considered hazardous or acutely so and pictures of the kinds of goggles recommended for different kinds of work.

Abbreviated laboratory safety rules from Memorial University of Newfoundland. They seem to be gone -- let me know if you find them on this site.

Excerpts from Genium's safety publications. This used to be a very good educational site but it is harder to find free stuff than it used to be. They used to have a nice essay on "What is an MSDS?"

General laboratory safety, including design, from Flinn Scientific, which produces lots of educational materials for high school labs. Excellent discussion of the ANSI standard Z87.1 for goggles for chemical splash protection, general educational laboratory safety and links to MSDS's. A good compaany and a good site.

What is an MSDS? Genium is a important supplier of safety information. This description is clear and well-written. They sell MSDS's so don't expect to find them for free on the site.

WWW resources for MSDS's from 3E, a leader in "hazmat" information, including an description of what MSDS's are and links to some good sites where you can read or download them.

MSDS's from the University of Vermont and the links it maintains to other sources of MSDS's and other safety information.

Oxford University's collection of MSDS's and a lot of other safety information.

MSDS's from Fisher Scientific: Search either the Acros Organic or Fisher Chemical Catalog for the compound; the description will include a choice for MSDS.

Cornell University MSDS collection, searchable by typing in the name.

The University of Georgia's Public Safety Division has links to a large number of universities and companies which have MSDS's posted as part of their commitment to Right-To-Know laws. Hazmat takes you to the msds sheets and links.

MSDS Search 2003 did not seem to have a large variety of suppliers or compounds.

MSDS Provider links to the manufacturers, as each has to publish the MSDS for each compound they sell (and each form of it). Here's your chance to learn about chemical manufacturers and distributors.

The American Chemical Society's Chemical Health and Safety Committee, with links to the magazine, videos, courses, and sites all over the world.

E-mail me at sweeting@midget.towson.edu with additions and corrections to this list.

Last update February 2, 2001