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JCE ChemInfo: Organic
Hans J. Reich University of Wisconsin–Madison Madison, WI 53706
Introducing JCE ChemInfo: Organic
Hans J. Reich Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706;
[email protected] Information for Organic Chemists
• Carbohydrates
“JCE ChemInfo: Organic” is a collection of Web pages containing information useful to teachers, researchers, and students in organic chemistry, biochemistry, and medicinal chemistry. The pages have been selected for ease of use, broad applicability, and quality of coverage. Topics will include structural information, organic reactions, nomenclature, physical properties, and spectroscopic data. These Web pages will be updated when possible and additional Web pages will be added as they become available. We encourage others who have collected data useful to organic chemists or who regularly use Web sites that provide such data to contribute their information to this column. An email message to the column editor, Hans J. Reich (reich@ chem.wisc.edu), should describe the data and explain their use.
• Steroids
Nomenclature Organic chemists delight in using acronyms and in naming important reactions, reagents, postulates, rules and effects after the chemists who first introduced or broadly applied them in the chemical literature. The resources below will help the mystified chemist who encounters such names in the literature. • Acronyms: about 150 common acronyms are listed along with their full names and structures • Named Reactions: This Web site lists 95 of the most important named reactions in organic chemistry. Each is linked to a Web page that gives the primary reference and equations for one or more recent literature examples that illustrate the use of the reaction. • Named Reagents: This convenient list provides structures of more than 160 common reagents used in organic chemistry that are often referred to by the originator’s name, by an acronym, or by a trade name. • Named Rules and Effects: Concise descriptions and structures of a number of named effects, rules, stereochemical models and hypotheses—from Baldwin’s rules to the Zimmerman–Traxler transition state— are given.
The International Union of Pure and Applied Chemistry has developed an extensive series of documents describing the nomenclature of organic compounds. Their recommendations have been summarized at these sites; the URLs listed on p 496 provide links to these sites. • Class Names • Organic Compounds • Physical Organic Terms • Bioinorganic Terms • Heterocycles
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• Stereochemistry
Many reactions of organic compounds involve reactive intermediates. This site (linked from the table on the next page) gives GIF structures of common ones. • Reactive Intermediates
NMR Spectroscopy Chemists engaged in any form of organic synthesis spend a good fraction of their time analyzing proton and carbon-13 NMR spectra to assign and confirm structure, establish conformational preferences, and determine the composition of mixtures. The links to the two sites below provide the chemical shifts and some coupling constants for thousands of organic compounds to serve as models for interpreting proton and carbon NMR spectra. Each collection is indexed by functional group and compound type, allowing individual compounds to be easily found and facilitating comparison of related structures. References to the source of the data for each compound are provided. A readily accessible collection of proton and carbon chemical shifts of this size is not available anywhere else— on the Web or in hard copy. • Proton Chemical Shifts •
13Carbon
Chemical Shifts
It is valuable to be able to see actual reproductions of spectra for comparison purposes, or for creating exercises and exam questions. The Web site below provides a free and convenient source of NMR, IR, and Mass spectra, including more than 12,000 proton and carbon NMR spectra, more than 20,000 mass spectra, and almost 50,000 IR spectra. The Web site provides numeric summaries of the data, but does not provide vector images of the spectra, which would be the most useful. However, a GIF image of the actual spectrum, which is adequate for the simpler spectra, can be downloaded easily. • NMR, IR, and Mass Spectra
pKa Values The pKa values of CH, OH, NH, and SH bonds in organic molecules have tremendous value for understanding and predicting many aspects of their reactivity. The rates of deprotonation, leaving group abilities, anion nucleophilicity, rates of anionic fragmentation, activation of double bonds towards nucleophilic addition, ease of single electron reduction, and reactivity of organometallic compounds all correlate strongly with pKas of the conjugate acids of the appropriate anionic species. The Web sites below provide many pKa values of organic molecules in three different media: in solution in DMSO, in aqueous solution, and in the gas phase.
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Bordwell pKa Values in DMSO: The late F. Bordwell of Northwestern University measured the pKa values of thousands of organic compounds. This Web site makes some of the data he measured conveniently available to the chemical community, and provides literature references to the published data (the Web site also includes much unpublished data).
Resources Aqueous pKa Values: This list was originally collected by W. P. Jencks and F. H. Westheimer and compiled by R. Williams. Gas Phase Acidity: This site provides a very comprehensive collection of thermodynamic data selected by the scientists at the National Institute of Standards and Technology (NIST).
Links to the JCE ChemInfo: Organic Collection Nomenclature Acronyms: http://www.chem.wisc.edu/areas/reich/Handouts/acronyms.pdf Named Reactions: http://orgchem.chem.uconn.edu/namereact/named.html Named Reagents: http://www.chem.wisc.edu/areas/reich/handouts/NameReagents/namedreag.htm Named Rules and Effects: http://www.chem.wisc.edu/areas/reich/handouts/Nameeffect/named-effects.htm Class Names: http://www.chem.qmw.ac.uk/iupac/class/ Organic Compounds: http://www.acdlabs.com/iupac/nomenclature/ Physical Organic Terms: http://www.chem.qmw.ac.uk/iupac/gtpoc/cont.html Bioinorganic Terms: http://www.chem.qmw.ac.uk/iupac/bioinorg/ Heterocycles: http://www.chem.qmw.ac.uk/iupac/hetero/HW.html Carbohydrates: http://www.chem.qmw.ac.uk/iupac/2carb/ Steroids: http://www.chem.qmw.ac.uk/iupac/steroid/ Stereochemistry: http://www.chem.qmw.ac.uk/iupac/stereo/ Reactive intermediates: http://www.chem.wisc.edu/areas/reich/handouts/Reactive-Intermediates.GIF
NMR Spectroscopy Proton Chemical Shifts: http://www.chem.wisc.edu/areas/reich/handouts/nmr-h/hdata.htm Carbon-13 Chemical Shifts: http://www.chem.wisc.edu/areas/reich/handouts/nmr-c13/cdata.htm NMR, IR, and Mass Spectra: http://www.aist.go.jp/RIODB/SDBS/menu-e.html
pKa Values Bordwell pKa Values in DMSO: http://www.chem.wisc.edu/areas/reich/pkatable/index.htm Aqueous pKa Values: http://research.chem.psu.edu/brpgroup/pKa_compilation.pdf Gas Phase Acidity: http://webbook.nist.gov/chemistry/acid-ser.html
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