Although there are many other sites, the following were selected to be probably the most useful found so far for each type of topic in Chem 226 and 227. If you find something better or something useful for a topic for which there are no listings, let your instructor know so that it might be included the next time this is updated.
Karen Long
Last updated July 2009

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Web sites

GENERAL REFERENCE DATABASES ON CHEMICALS (STRUCTURE, PROPERTIES, HAZARDS, SPECTRA):

ChemIDplus http://chem.sis.nlm.nih.gov/chemidplus/ from the United States National Library of Medicine. A properties database searchable by name, structure (drawn by you on the site), formula, registry number, etc. Structure search uses MarvinSketch (click on the Marvin window to start the software). You can also search for all compounds that have a particular melting point or boiling point range. Property data includes melting point, boiling point, solubility, pKa. Some toxicity data available. No spectra.

ChemSpider http://www.chemspider.com/ - maintained by the Royal Society of Chemistry, UK. Another physical properties database searchable by name, structure (drawn by you on the site), formula, registry number, etc. To search by drawing the structure, go to Structure Search (side menu) then click on the structure shown and click on the Edit tab. Properties include melting point, boiling point, solubility, refractive index. Predicted boiling points, etc, may be available even if experimental data is not. Need to create an account and login to get any spectra that are available.

NIST Chemistry WebBook http://webbook.nist.gov/chemistry/ - from the National Institute of Standards and Technology, USA. Another properties database searchable by name, structure (drawn by you on the site), formula, registry number, etc.. Property data includes melting and boiling point and IR, UV, and MS spectra of some compounds. Many of the IR spectra are taken in the gas phase, however, which often looks different from the liquid and solid phase spectra we take.

Vermont SIRI (main site) http://hazard.com/msds/ - This is a searchable database of Material Safety Data Sheets (MSDS) from a large number of manufacturers. You just type in the name of the compound. Mallinckrodt Baker's sheets are particularly user friendly and often contain the easy to understand SAF-T-DATA(tm) ratings. The home page also contains a searchable version of Genium's MSDS Pocket Dictionary for easy to obtain definitions of safety terms. If this site is down, try the link below or try the manufacturer site directly. Mallinckrodt Baker is http://www.mallbaker.com/americas/catalog/default.asp

Safety Emporium Internet Resources for MSDS, http://www.ilpi.com/msds/index.html#Internet - a list of links to more MSDS sites if you need it. Also a link to another MSDS terms glossary

SDBS, the Spectral Database System http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng - The Spectral Database System is organized by the National Institute of Advanced Industrial Science and Technology (AIST), Japan. Search by name, formula, or registry number for IR, H1 NMR, C13 NMR, and MS spectra or data. You can also search by peaks on the spectra.

SigmaAldrich.com http://www.sigmaaldrich.com/technical-service-home/product-catalog.html Spectra, properties, and MSDS are available for many of the compounds that Sigma/Aldrich sells. You can search for the chemical by name, structure (drawn by you on the site), molecular formula, CAS number, etc. To get to the structure-drawing program (JME editor), select Substructure in the search type menu. When you get to the compound, click on the order number for one brand of the compound. Links to available spectra are on the side. For IR, choose FT-IR-condensed phase, not FT-IR-Raman.

Database of NMR Spectra http://www.nmrdb.org/ - from Ecole Polytechnique Federale de Lausanne. This site allows you to draw the structure of a compound (JME Editor) and get a simulated NMR spectrum. You can also use the applets to help assign an NMR spectrum to a compound.

Science and Fun Spectroscopic Tools http://www.science-and-fun.de/tools/ - Provides "Wizards" for IR, NMR (¹³C and ¹H), and MS. You type in a location on the spectrum and it gives some possible assignments for that peak. Basically it's a searchable reference table. Especially useful for providing suggestions for mass spectrum fragment formulas from the mass of the ion.

Molecules to Go (Molecules R Us) by the National Institutes of Health http://molbio.info.nih.gov/cgi-bin/pdb - a searchable database of protein structures, in pdb file format, which can be viewed and studied using MarvinSpace, Chime, RasMol, or other pdb viewer.

ANIMATIONS, TUTORIALS,ADDITIONAL PROBLEMS, AND READINGS ON MULTIPLE TOPICS IN OUR TEXT

Tutorials by Dr. Thomas Poon, Claremont Colleges http://ochem.jsd.claremont.edu/tutorials.htm# There are two types of excellent Tutorials.

(1) The PreLecture series is a set of movies with audio narration. Explains conformational analysis, resonance structures, mechanism writing, degrees of unsaturation, spectroscopy, nucleophilic acyl substitution, and many more topics. Segments are mostly10-20 minutes. Requires free downloadable QuickTime viewer. (Can also be obtained as podcasts.)

(2) The Shockwave Animations are a set of animations with text narration on a variety of topics (16 areas) for the course. You may need to download Shockwave (free) to use these. Click in screen to start and go to next "slide" when there is no "continue" button.

Synthesis Explorer in the UC Irvine ChemDB. http://cdb.ics.uci.edu/CHEM/Web/index.htm Go to the Reaction Explorer section. You can create and solve synthesis and mechanism problems based on criteria you set up. Watch the introductory videos before using.

Organic Chemistry Online by Dr. Paul R. Young, University of Illinois,Chicago - Lecture notes on many course topics if you need more reading. Most useful for additional problem drill. You need to write down your answers on paper, then click for the answer.

Practice Problems by Dr. Thomas Poon, Claremont Colleges http://ochem.jsd.claremont.edu/practice.htm - Problem worksheets for various topics with answer keys.

Organic Chemistry Practice Problems by Dr. William Reusch of Michigan State Universtiy http://www.cem.msu.edu/~reusch/VirtualText/Questions/problems.htm Good problems in many course topics with answers, hints, and links to an online text. Some require you to draw the answer with the provided molecule drawing program (JME). Questions color coded for level.

Organic Chemistry by Jennifer Muzyka http://web.centre.edu/muzyka/organic/organic.htm Animations of molecules illustrating several concepts, problems, tutorials, spectroscopy problems.

Organic Reaction Quizzes and Summaries http://pages.towson.edu/ladon/orgrxs/reactsum.htm
Dr. Linda Sweeting, Towson State University, includes summary lists of reaction and syntheses of numerous functional groups.

Reaction Finder for The Organic ChemIST http://www.stolaf.edu/depts/chemistry/courses/toolkits/247/practice/medialib/data/
- a site that can generate quizzes or single questions (with answers) on reactions from any specified chapter or topic in the usual organic textbook. A different format for selecting type of questions is at http://www.stolaf.edu/depts/chemistry/courses/toolkits/247/practice/medialib/data/quiz.htm

LAB TECHNIQUES (information and movies)

MIT OpenCourseWare - Digital Lab Techniques, http://ocw.mit.edu/ans7870/resources/chemvideo/index.htm - good videos with audio explaining the techniques of extracting and working up a reaction, using a rotary evaporator, melting points, filtration, recrystallization, sublimation, thin layer chromatography, column chromatography, refluxing, and simple, fractional, and vacuum distillation. Need RealPlayer to view

Chemistry, UCLA Office of Instructional Development. http://www.oid.ucla.edu/Webcast/chemistry/index.html - good videos with audio (about 15-20 minutes each) explaining the techniques of extraction, melting points, recrystallization, simple distillation, fractional distillation, thin layer chromatography, gas chromatography, column chromatography, spectrophotometric analysis, and infrared spectroscopy. Need RealPlayer to view.

The Interactive Lab Primer, http://www.rsc-teacher-fellows.net/, managed by the Royal Society of Chemistry Teachers, UK. Contains many excellent videos on lab techniques and animations of the process occurring when the technique is used. Techniques with videos include: assembling apparatus, thin layer chromatography, column chromatography, simple, fractional, steam and vacuum distillation, drying liquids, hot gravity and vacuum filtration, infrared spectroscopy, melting points, recrystallization, reflux, use of the rotary evaporator, and others.

The Virtual Lab Tutor, http://ochem.jsd.claremont.edu/lab.htm# by Dr. Thomas Poon, Claremont Colleges. Videos and text directions on how to do melting points, distillation, drying with a drying agent, recrystallization, reflux, filtration, rotary evaporation, thin layer chromatography, and column chromatography. Need QuickTime to view these.

CU Boulder Organic Chemistry, http://orgchem.colorado.edu/hndbksupport/GC/GC.html - good pictures and a video of how to run a GC (see link in second paragraph - need RealPlayer).

Nomograph for calculating boiling point at one pressure from the boiling point at another pressure http://www.sigmaaldrich.com/technical-service-home/product-catalog.html
Type nomograph in the search box to get to the nomograph. Very useful for vacuum distillation.

The Polarimeter. http://scholar.hw.ac.uk/site/chemistry/activity5.asp from Heriot Watt University - how the polarimeter works

RESEARCH SEARCH

Google Scholar http://scholar.google.com/ This is a search engine for only scholarly papers on the web. Eliminates a lot of junk!

Scirus Search Engine for Science http://www.scirus.com Search the web and professional journal articles on scientific topics of all types, including chemistry, biology, physics, medicine, etc. Links available to free abstracts of most journal articles (although you may have to register at some sites). For most full text articles you would have to pay. Can refine your search, for example looking only at references on double blind controlled medical studies on the effect of a certain medicinal or only at the biosynthesis applications of a Claisen condensation, etc. Can also search for only specified publication years if desired.

National Library of Medicine: http://sis.nlm.nih.gov/
Contains many useful databases of health related information. Check out especially:
Toxnet http://toxnet.nlm.nih.gov/ - a cluster of databases on toxicology, hazardous chemicals and related areas
PubMed Medline http://www.pubmed.gov Search about 12 million medical and life science journals back to 1960 and provides abstracts for most articles and full text for a few.
MedlinePlus http://www.medlineplus.gov/ A consumer health section explaining various health issues. Drug information available and more.

TUTORIALS, PROBLEM SETS, ANIMATIONS ABOUT SPECTROSCOPY (Chem 227)

Organic Structure Elucidation-A Workbook of Unknowns by Prof. Bradley Smith, Notre Dame www.nd.edu/~smithgrp/structure/workbook.html - Contains 64 unknowns to identify using all the spectroscopy types in combination. Ranked as Easy, Moderate, and Difficult. Some of these were assigned as part of your spectroscopy worksheet to turn in. Answers are not given

¹H NMR Interpretation Tutorial by S. Bruce King, Wake Forest University http://www.wfu.edu/~ylwong/chem/nmr/h1/ - practice predicting and interpreting NMR spectra, tutorials, review. Must have Shockwave installed.

¹³C NMR Interpretation Tutorial by S. Bruce King, Wake Forest University http://www.wfu.edu/%7Eylwong/nmr/c13/ - practice predicting and interpreting NMR spectra, tutorials, review. Must have Shockwave installed.

WebSpectra by Prof. Merlic, UCLA http://www.chem.ucla.edu/~webspectra/ - a collection of spectra problems with answers (but not explanations) ranked by difficulty. All have ¹³C and ¹H NMR spectra, some have IR. Tutorials also available.

The Mass Spectrometer Simulator from the Organic Chemistry Virtual Tutor by Dr. Thomas Poon and Bradford Mundy, Colby College http://www.colby.edu/chemistry/OChem/DEMOS/MassSpec.html - animated graphics showing the parts of the mass spectrometer

OTHER.

Dr. Duke's Phytochemical and Ethnobotanical Database from the Agricultural Research Service, Beltsville, MD http://www.ars-grin.gov/duke/ - Very useful for Essential Oils Lab. Can use search engine to find compounds and amounts in a plant when given the common name (like bay laurel) or scientific name. Can find biological properties of those compounds, other plants with the same chemical in order of amount, etc. Contains reference to a lot of plants.

Organic Chemistry Exams by Dr. Thomas Poon, Claremont Colleges. http://ochem.jsd.claremont.edu/hints.htm Series of past O-Chem class exams at the Claremont Colleges. Answer keys included. The course is a comparable level to ours but topics in each section may vary because we are using a different textbook.

Organic Chemistry Songs mostly from students in Dr. Otto Phanstiel's classes at the University of Central Florida http://organicsongs.cos.ucf.edu/

InnoCentive, http://gw.innocentive.com/ar/discipline?categoryName=Chemistry - This is a site where companies and entrapreneurs post problems they want solved and rewards (usually $10,000 or more) for the best solution. Interesting to look at even if you don't feel you have the background to work on the problems competitively yet. You have to register.

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Software for your home computer

The following software tools will be useful for assignments in Chem 226 and 227. They will be available on specified campus computers. If you have a home computer, you might like to download these free from the Web to your home computer. The software is available in both Mac and PC formats.