How to use this program

There are two ways to use this application.

The first way is to input as much information as you can and then hope that the search yields just a few possible trial structures. Because many substituent constants are similar, hundreds of different substitutent patterns will give the same chemical shift. Therefore, one chemical shift will match many possible chemical environments. This approach is most successful if you know the formula and the functional groups that are present. You are most likely to get just a few possibilities if your chemical shift is large.

The second way to use this application is to say "what-if". "What-if" a carbonyl is near? What structures would match my chemical shift? "What-if" a carboxylic acid group is near? Or, if you can't tell if your -CH2- protons are equivalent or not, "what-if" they are inequivalent? Or "what-if" my -CH3 group is part of an isolated ethyl group?

Whichever approach you take, using this program will help to spark some ideas for possible structures. One of the biggest pitfalls in spectral interpretation is falling into the trap of not considering all possibilities. Using this program will help to free up your decision making by helping you to look at multiple possibilities.

Mass Spectrometry and Elemental Analysis

The parent mass is the mass of the molecular ion from the mass spectrum. The parent mass limit helps to determine how many substituents to look for. The parent mass is very helpful for small molecules. (The program uses the term parent mass instead of the molecular weight, because of the rounding rules that are inherent in unit mass resolution MS.) Knowing the exact formula is a powerful tool for narrowing down the possibilities. First of all, the formula limits the types of functional groups to look at. For example, if the formula has only one oxygen, then carboxylic acids are not possible.

More importantly, the exact formula allows the calculation of the number of double bonds and rings, dbr. Some authors call the number of double bonds and rings the degree of unsaturation. If the trial formula is CcHhOoNn then the number of double bonds and rings is:

     dbr = (2c-h+n+2)/2

For example, the number of double bonds and rings for benzene is 4. This parameter helps to narrow down the functional groups that are possible and helps in screening possible trial strucutres. For example, if the dbr for your compound is 3, then you can't have an aromatic ring present. The dbr is also helpful in prediciting the spin-spin multiplicity of a trial structure. For example, if your compound has dbr=2 and you have two unsaturated function groups, then there can't be any rings. If there are no rings or chiral centers then -CH2- geminal protons will be equivalent.

Chemical Types

You can often decide on functional groups from the IR and mass spectra. Your search will go much faster if you can rule out certain substituents. Select these as absent. You also might suspect that a given functional group is near to your proton. This knowledge will greatly decrease the number of trail structures that fit your chemical shift. For this program, near means alpha or beta to your proton. So, if the program isn't able to get through a full search before it finds 20 possible structures, use the "what-if" approach while specifying possible near substituents.

Multiplicity Information

The multiplicity of your peak can be the most powerful way of screening possible structures. The program makes some rough assumptions about each trial structure and tries to guess the multiplicity. A score is then calculated for the fit between your input multiplicity and the calculated multiplicity for the trial structure, with 4 being best score and 1 the worst fit. The minimum, expected, and maximum multiplicity are then printed. The minimum multiplicity assumes that all of the coupled protons are equivalent:

     minimum multiplicity = n+1 , where n=total number of coupled spins

The expected multiplicity assumes some rough values for the J coupling constants, and groups equivalent spins by their J's. The maximum multiplicity assumes all the groups of equivalent protons are distinct. These three guesses are printed in the order minimum < expected < maximum. If the program is assuming a J4 W coupling for the maximum multiplicity, a W will be printed. More information on the scoring is available, below.

Displaying Your Structures

After you click on Submit, all possible trial structures will be tested, until 20 structures have been found. These 20 will be listed in the selection box. To see the structure, click on the corresponding line in the selection box. A new window will open with the structure displayed. ( I apologize for the quality of the output; if you know how to easily get better output, send me mail.) You can leave this window open as you click on other options. Just pull the stucture window so that it doesn't overlap with the main window.

Multiplicity Scoring

The program assumes the coupling constants for beta protons are either 2 or 6 Hz. Geminal protons in methylene groups are assumed to have a distinct coupling constant. Gamma protons, for example on acetylene and vinyl substituents are assumed to have 2 Hz coupling constants. The expected multiplicity is then:

     expected multiplicity = (n2+1)*(n6+1)*(ngem+1)

     where n2=number of spins with J=2Hz, n6=number of spins with J=6 Hz, and ngem = 1 for inequivalent -CH2- groups.
The program checks the "equivalent/inequivalent" selection and the number of double bonds and rings (dbr) for the trial structure to determine if geminal coupling is possible.

The maximum multiplicity assumes all the groups of equivalent protons are distinct. In other words, the assumption is that all the vinyl protons are inequivalent, all methine protons are inequivalent, all the methylene protons are inequivalent if rings or chiral centers are possible, and all methyl groups not on the same carbon are inequivalent:

     maximum multiplicity = (nMe+1)*2n'

where nMe is the number of vicinal methyl group protons and n'=n-nMe.

if the input multiplicity = expected : score = 4
if the input multiplicity is close to the expected : score = 3
if the input multiplicity > expected*2 : score = 2
if the input multiplicity < expected/2 ) : score = 1

List of Substituents and Literature References

Colby College Chemistry, T. W. Shattuck, 2000