Organic Chemistry Related Websites

Comprehensive Indices to Chemistry Websites

Organic Chemistry Resources Worldwide -- Lots of links, broken into 6 major subcategories: The Literature, The Bench, Structural Analysis, The Desk, Communication, Other Activities.

The Virtual Chemistry Center -- Lots of links to material from every branch of chemistry, broken into several categories: Measurement, Periodic Tables, Chemicals and Biochemicals (Major Databases and Specialized Databases), Chemistry Overview, and Chemistry Courses, Textbooks, and Databases.

Organic Chemistry Portal -- Main categories: Organic Reactions, Org. Chem. Highlights, Abstracts, Chemicals, Chemistry Tools, Chemistry Books, Resources.

Comprehensive Lecture Related Websites:

WEB-sters' Organic Chemistry -- This website contains links to all sorts of useful web pages for students of organic chemistry. This is a great place to start your search for online resources to help you in organic chemistry.

Organic Chemistry Online at the University of Illinois at Chicago -- This website contains reviews and problem sets on a variety of topics discussed in first semester organic including: Structure & Bonding, Spectroscopy, Stereochemistry, and Functional Group Reactions.

Organic Online -- Try out the online quiz feature at this web site.

Organic Reaction Quizzes and Summaries -- This site has a summary of reactions for organic chemistry students. It also has quizzes so you can practice recognizing reactions.

The Organic Chemistry Student Resource Page at Colby College -- Although some of the material at this website is specifically directed towards the Colby chemistry program, there is also a wealth of material that will be useful to you. Some categories that you might want to investigate are: Stereochemistry, Practice Problems, Links to other websites, Computer Demos, and Organic Webcards.

Spectroscopy -- Tutorials and Practice Problems

• Organic Chemistry Online at the University of Illinois at Chicago -- This site has good introductions to IR Spectroscopy, NMR Spectroscopy, and Mass Spectrometry.
  
  
• Organic Structure Elucidation Workbook -- This online workbook contains 64 spectral problems grouped into three classes: easy, moderate, and difficult. Most problems contain an IR spectrum (film or KBr pellet), a 500 MHz 1H NMR spectrum, a 125 MHz 13C NMR spectrum, and a 70 eV electron ionization Mass Spectrum.
  
  
• WebSpectra - Problems in NMR and IR Spectroscopy -- This site has a number of problems grouped into four categories: beginning, intermediate 1, intermediate 2, and advanced. All problems contain 1H-NMR and 13C-NMR spectra, some also contain IR, DEPT, or, COSY data. There are also a number of educational pages describing IR and NMR spectroscopy.
  
  
• Predicting Spectra for Nuclear Magnetic Resonance (NMR) -- Dr. Tom Ippoliti and the Center for Multimedia Development at the University of St. Thomas have developed this web tutorial for undergraduate organic students. The exercise begins by presenting a molecule with a highlighted fragment. The student is asked to predict three qualities of the associated signal: the chemical shift (the signal’s position along the axis), its integration (the area under the signal), and its splitting pattern (the number of "peaks" the signal has). The program is adaptive and presents more difficult problems as the student masters simpler ones. This site also provides an online NMR shift reference table, a shift calculator, and tutorials on predicting shift and splitting.
  
  
• Univ. of Arizona MS tutorial -- This is an excellent introductory tutorial for students learning Mass Spectrometry. It includes a brief introduction to Mass Spectrometry and how it works, a short list of the basic steps used to interpet a mass spectrum, examples of analyzed fragmentation patterns observed for molecules containing common functional groups (alcohols, aldehydes, alkanes, amides, amines, carboxylic acids, esters, ethers, halides an ketones), and an excellent set of quizzes.
  
  
• Mass Spectroscopy for Chromatographers at Univ. of Akron -- This is an introductory "short course" in the use of the mass spectrometer attached to a gas chromatograph. The section titled "Mass Spectrometer Detector" discusses some of the instrumental details. There is also a section on Mass Spectral Interpretation, and an excellent set of 5 example problems that take you through the process of analyzing a mass spectrum. I recommend looking at these.

Lab Related Websites:

Physical and Safety Data for Organic Molecules

• MSDS Websites -- The sites listed here contain online MSDS (Material Safety Data Sheet) information. These sites are useful sources of safety information and physical data on a wide variety of compounds. The UPS chemistry department maintains MSDS's in Mike Hottott's office, Th 308a.
  
  
• Chemfinder -- This site lets you search for compounds by name, formula, MW, mp, bp, CAS #, structure or substructure. [To do the structure searching you will need to use a Smiles String representation of your structure or substructure. The smiles string can be automatically generated by downloading the drawing program (CS ChemDraw Net) that will alow you to save a structure as a Smiles String.] In addition to giving you information about the compound(s) it finds, this site also provides links to other chemistry sites that have information about the compound.
  
  
• Organic Compounds Database -- This database allows you to search for compounds by mp, bp, index of refraction, MW, formula, UV absorption, mass spectral peaks, and chemical types (carbonyl, aromatic, NH/OH, saturated or unsaturated CH). It then gives you a list of compounds that meet your criteria. You can then select a compound and get all the information listed above.
  
  
• Chemexper -- This site has a chemicals directory that can be searched by registry number, molecular formula (exact and non-exact), and chemical names (and synonyms). The information you get is similar to that found in the Aldrich catalog: structure, MW, mp, bp, density. It may also provide a link to MSDS's for the compound. This site also includes a Formula Weight Calculator.
  
  
• NIMC Spectral Database System -- This Japanese database is the most complete and useful web-based spectra archive for organic chemistry that I have found. You can search for data on specific compounds based on compound name, molecular formula, number of atoms (CHNO), molecular weight, or CAS registry number (you must append the % symbol to the registry number). This database contains:
  • Mass spectra (19,000)
  • FT-IR spectra (47,000)
  • 90 MHz and 400 MHz ¹H-NMR spectra (11,500)
  • ¹³C-NMR spectra (10,200)
  
  
  
• NIST Chemistry WebBook -- NIST is the National Institute for Standards and Technology. You can search for data on specific compounds in the Chemistry WebBook based on name, chemical formula, CAS registry number, molecular weight, or selected ion energetics and spectral properties. This site contains:
  • IR spectra for over 5000 compounds
    • Most of the IR Spectra in this database are in the vapor phase, and they often look significantly different from those acquired on neat liquids. I recommend checking the NIMC Spectral Database listed below first, since the spectra given there will more closely resemble the ones that you acquire.
  • Mass spectra for over 10,000 compounds
  • Thermochemical data for over 5000 organic and small inorganic compounds
  • Reaction thermochemistry data for over 8000 reactions
  • Electronic/vibrational spectra for over 2000 compounds
  • Constants of diatomic molecules (spectroscopic data) for over 600 compounds
  • Ion energetics data for over 14,000 compounds
  • Thermophysical property data for 16 fluids
  
  
  
• University of Potsdam -- Spectroscopic Tools -- This site lets you type in a ¹H-NMR chemical shift, IR absorption, or ms fragment and it will give you a list of possible structures that could give rise to that signal. There is also a large amount of information on NMR available at this site or the Univeristy of Potsdam NMR Home Page. This includes:
  • ¹³C-NMR Shift calculation
  • NMR Periodic Table
  • NMR Solvent Information
  • Chemical Shift Tables for ¹H, ¹¹B, ¹³C, ¹⁵N, ¹⁷O, ¹⁹F, and ³¹P.
  • ¹³C-NMR Database (192 compounds only).
  • Two spin NMR lineform simulation
  • Table of Proton NMR J-couplings

Writing Lab Reports

• Writing as A Scientist -- Resources from Collins Library

Drawing and Modeling Programs Available on the Web

• ChemDraw -- ChemDraw is the premier chemical structure drawing program. The University of Puget Sound has purchased a site license for the program (Std edition), which means that any student or faculty member may download and use this program on their own computer. (You need to have a UPS email account in order to activate the program.
) The program will also be available on lab computers in the chemistry department.


• ISIS Draw -- This is a free chemical structure drawing program for both Macintosh and Windows computers. This is the best deal going! Click here to download this program.
  
  
• Chemscape Chime -- This is a free Web browser plug-in that can display 2D and 3D structures embedded within an HTML page or table. Click here to download this program.
  
  
• RasMol -- RasMol is free software for looking at molecular structures. It is similar to Chime (above) but runs as a separate application rather than as a window in a web browser. It runs on Windows or Macintosh/PPC computers. (also unix).

Other Chemistry Websites

• The Basics of NMR by Joseph P. Hornak -- This is an online book describing the principles of NMR (Nuclear Magnetic Resonance Spectroscopy). This is an excellent discussion of both the theory and some practical considerations regarding NMR spectroscopy. Table of Contents: Introduction, The Mathematics of NMR, Spin Physics, NMR Spectroscopy, Fourier Transforms, Pulse Sequences, NMR Hardware, Practical Considerations, Carbon-13 NMR, 2-D Techniques, Advanced Spectroscopic Techniques. He also has an online book on MRI (Magnetic Resonance Imaging).