Thomas Vosegaard
Interdisciplinary Nanoscience Center and
Department of Chemistry
Aarhus University, Denmark
iSpec is a program developed to train student's skills in analyzing spectroscopic data to reveal the structure of small organic molecules. It should be seen as a supplement to the classic exercises where a set of spectra is analyzed in order to obtain.
With iSpec we wish to train the student's understanding of the resources involved in acquiring the experiments and performing the analysis. It is designed as a game, where the player has some available resources - defined as a number of resource points (RP) - for each exercise. Each spectrum costs resources, and in iSpec they can be purchased by resource points. In addition, time may be considered a resource, just as submitting a wrong answer costs resources.
It is thus the player's choice which spectra to obtain in order to provide a qualified answer. A correct answer to the exercise is awarded a number of resource points. By submitting the correct answer, the exercise is solved, and the available RP is transferred to the user as experience - as experience points (XP).
Once the exercise is solved, there may be a couple of questions to answer. Correct answers are awarded with XP. The game can be played on computers or mobile devices. The layout is different on mobile devices because of their generally reduced screen sizes.
The iSpec game is accessed through the web site ispec.pastis.dk. This web site brings up the following blank window
Use the unique link provided to you in the registration email to proceed. This will allow you to specify a new password. Once logged in, you will see a window similar to this
where the avaliable exercises are listed. Note that the number of exercises may change during the semester as exercises may be released at different times.
For each exercise its name, current status, and resource points are given. Note that the exercises are grouped for easier navigation between them. Your administrator decided which exercises you can access.
An exercise may be in one of the following modes
| New exercise |
| Combat mode |
| Training mode |
| Done - the exercise is solved and the questions are answered |
A game is started when you either select to start it or when you unlock a spectrum. When the game is started, it automatically changes from New to Combat mode. In Combat mode, everything is considered a resource. (i) Obtaining spectra takes time and is hence a resource. (ii) Analysis of spectra takes time, which is also a resource. (iii) Making wrong guesses typically wastes other people's time and is therefore also considered a resource spent. In iSpec, the use of resources means spending resource points (RP).
If you solve the exercise while you still have RP left, the game changes to Solved mode. If you don't manage to solve it in time, the game changes to Training mode, where all spectra are unlocked, guesses are free, and you will have optional hints to guide you to the correct solution. Once you find the correct solution, the game changes to Solved mode.
Your motivation to do a great job is that any RP from the exercise is transferred into experience points (XP) when you have solved the exercise. See how many experience points you can get - and beat your friends.
In solved mode, there may be a few questions you can answer to gain further XP. If you fail to answer, the number of possible XP is reduced.
When selecting an exercise, you will obtain the window shown above. On the top you see a menu with a set of buttons allowing you to perform various operations. The buttons have the following functions
| Submit solution |
| Start/pause game |
| Open a J-coupling simulator window |
| Open a formula calculation window |
| Open a benzene shift calculation window |
| Show open windows. This is mostly relevant if playing on a mobile device. |
The window titled General on the left shows the control of the game. First your credentials and total number of experience points. Then some info on the exercise: (i) The name of the exercise and how many RP are available, (ii) how many RP are left, (iii) how much time did you spend on the exercise. Below this is a list of available spectra. Each spectrum may either be locked or unlocked. To unlock a spectrum, you will spend the amount of RP listed. At the bottom of this window you have two additional items that are unpopulated initially. Help in the form of hints will appear when you go into training mode, and questions will appear when you have solved the exercise. The More info container will be populated with spectrum metadata as you unlock spectra.
On the following screenshot, I have unlocked the 1H NMR spectrum and the MS spectrum. Furthermore, I have resized the NMR spectrum window, zoomed in on a region of the spectrum, and performed peak picking and integration using the buttons below the window title.
As soon as a spectrum is unlocked, the game starts, i.e. it enters Combat mode. Time is running at the cost of 1 RP per minute. Note that when I unlocked the MS spectrum, I also got the M/z value with two digits for the peak at 94 mass units. If I would like to have the mass of this peak with a higher precision (4 digits), I can buy it. These features only apply to some of the exercises. The philosophy here is that when you do an MS experiment in the lab, you automatically get the peak positions with ca 2 digits precision, while you need to do extra experiments to get better precision (e.g. 4 digits).
Once you have analysed all spectra and are ready to submit a solution, use the Molecule window to draw a molecule as illustrated above. Do not draw any explicite hydrogen atoms. Functional groups may be found in the FG menu.
When you feel that you have the right molecule, you may submit your solution by hitting the button . Note that a wrong solution will cost you 5 RP.
If you have spent all of your RP on unlocking spectra, making wrong guesses, or used too much time looking at the spectra, so you have RP = 0, the game mode changes from Combat to Training mode.
In Training mode, all spectra are unlocked, so you have everything available. In addition, you may have some hints available from the General window on the left. Click on the hints link to get the following window. By help from the hints, you should be able to solve the exercise.
When the game is solved, you will have the possibility to obtain extra experience points by answering a few questions related to the experimental spectra. Correct answers are awarded with XP, but the amount of XP you can obtain decreases if you answer wrong.
There are three utility functions you may like to use to speed up the analyses. They are explained below.
The benzene chemical shift calculation window looks as above. Select appropriate functional groups from the dropdown menus when hitting the individual substituents on the ring. The calculator is a simplified version of the one on our web site. The version on the web site offers insight into the underlying database of chemical shift contributions from the different functional groups.
The J-coupling calculator allows you to calculate coupling patterns of various coupled atoms. Simply select the coupling size and multiplicity, then the calculator will calculate the spectrum. Note that it assumes weak couplings.
If you know the molecular mass of a compound, you may guess which composition it has, as isotopes have slightly different masses. Typically, you need to know the mass with 2-4 digit precision to get a good guess of the brutto formula for the compound. In the M/z window, you can enter the mass, and the tool provides you with possible solutions. For your help, it also provides the number of double-bond-equivalents (DBE). For the molecular formula CcHhNnOoXx (with X representing halogen atoms), the number of DBE's is
\begin{equation} \mathrm{DBE} = c + 1 - \frac{h}{2} + \frac{n}{2} - \frac{x}{2}\label{eq:dbe} \end{equation}