Web Materials for Chem 226 and 227 (last updated 7/30/2012)
| Web sites | Software |
David Klein, Organic Chemistry Student Companion Site, http://bcs.wiley.com/he-bcs/Books?action=index&bcsId=6581&itemId=0471756148 . Contains many tutorial and problem solving videos by David Klein, interactive practice problems, and the list of errors in the textbook. FREE.
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 (now called Avantor) sheets are particularly user friendly and often contain the easy to understand SAF-T-DATA(tm) ratings.
MSDS Search http://www.msdssearch.com/dictionaryn.htm - the searchable Genium pocket dictionary of MSDS terms is on this site.
Occupational Safety and Health Administration, http://www.osha.gov/ - MSDS and other information
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://helixweb.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
Long's Short Secrets for Solving Hard Chemistry Problems - Organic Chemistry by Dr. Karen Long, Diablo Valley College http://voyager.dvc.edu/%7Eklong/ochemvideos/Videos.html Videos and associated handouts on select topics: "Representing electron movement using arrows", "Allene Chirality", the Alpha Carbon song.
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. To view as podcasts on mobile devices go to http://itunes.apple.com/podcast/organic-chemistry-prelectures/id173199626?mt=2|
|(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.|
Organic Chemistry Online by Dr. Paul R. Young, University of Illinois,Chicago http://www.askthenerd.com/ocol/#- Very useful for additional problem drill for all topics in the course. Version 2.0 is the easiest to use. You need to write down your answers on paper, then click for the answer. Review notes on many course topics are available also.
Practice Problems by Dr. Thomas Poon, Claremont Colleges http://ochem.jsd.claremont.edu/practice.htm - Good problem worksheets for various topics with answer keys.
Virtual Textbook of Organic Chemistry with Practice Problems by Dr. William Reusch of Michigan State Universtiy http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/intro1.htm A complete online textbook for extra information or comparison. Good problems in many course topics with answers, hints, and links to the online text http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Questions/problems.htm Some problems 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, nice reaction review problems to practice remembering reagents (Reaction Zoo), 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 giving examples of use of organic chemistry vocabulary words. It can also generate quizzes or single questions (with answers) on reactions from any specified chapter or topic in the usual organic textbook (the two textbooks referenced are texts we have used in our course in the past). A different format for selecting type of questions is at http://www.stolaf.edu/depts/chemistry/courses/toolkits/247/practice/medialib/data/quiz.htm
Practice on R and S designation of absolute configuration. http://chemistry2.csudh.edu/organic/startnewrands.html
- a site that gives various problems on designating R and S at a single
chirality center. Checks your answers, telling you priorities and
whether it is R or S. MUST USE INTERNET EXPLORER AS THE BROWSER.
LAB TECHNIQUES (information and movies)
MIT OpenCourseWare - Digital Lab Techniques, http://ocw.mit.edu/resources/res-5-0001-digital-lab-techniques-manual-spring-2007/videos/ - 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/ - 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.chem-ilp.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.
Nomograph for estimating boiling point at one pressure from the
boiling point at another pressure http://www.sigmaaldrich.com/chemistry/solvents/learning-center/nomograph.html
Very useful for vacuum distillation.
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/%7Ewebspectra/ - 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
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.
Chem 226 Organic Chemistry by Dr. Ron Rusay. http://www.chemconnections.org/organic/chem226/ More information and resources relevant to our course.
InnoCentive, http://www.innocentive.com/ - 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.
Organic Chemistry Songs from students in Dr. Otto Phanstiel's classes at the University
of Central Florida http://med.ucf.edu/ophansti/organic-songs/
|.||.||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.
||Marvin Beans (Marvin Sketch, Marvin View, Marvin Space)|
|The Marvin Sketch software enables easy drawing of organic molecules on the computer for incorporation into reports or other materials. It is also often used in web applications. The Marvin Space software enables you to view and rotate in three dimensions something drawn in Marvin Sketch or most other structure files on the web. Both of these are part of the Marvin Beans package. These packages have many other functions available, such as naming drawn structures and measuring distances between atoms. The software is available free from ChemAxon but you must register and give your email. In the past, some students have had problems if they didn't use a .edu email address. So I'd recommend that you use your district Insite email address.|
||JME Molecular Editor|
|by Peter Ertl at Comenius University Bratislava and later enhanced
at Ciba-Geigy Basel.
Another free structure drawing program which can be used on your computer. Also often seen in web applications.
|Logger Pro -data manipulation software|
|You can get a demo version (limited time usage) of the software we use on the lab computers to obtain and analyze gas chromatography data. Most of the time you can do your analysis in lab or the PS110 computers but this software is also available from Vernier for your home computer if desired.|