Mass Spectrometry (MS or Mass Spec) is an analytical technique where a sample is ionized and the mass of the resulting charged species are measured, usually with isotopic resolution. Electron Ionization (EI) is a common technique to ionize a sample, but it typically fragments the molecules into various smaller parts and EI is limited to compounds whose boiling points are less than 250°C. Electrospray Ionization (ESI) is another common technique, which does not result in fragmentation and gives the mass of the whole molecule, although the mass peak is often split because of naturally occurring isotopic abundances. Mass Spec is not a common instrument in the typical undergraduate organic laboratory, but the Virtual ChemLab simulation provides actual Mass Spec data for a wide variety of compounds. Mass Spec is a powerful analytical tool since it gives the mass of the unknown compound, but interpreting Mass Spec data is not necessarily straightforward.
As with the other spectroscopic techniques in Virtual ChemLab, a Mass spectrum can be measured on the solution contained in any flask or the separatory funnel after a reaction mixture has been worked up. Most of the Mass spectra that are given in the simulation were obtained from various national databases or predicted using advanced prediction algorithms. In general, EI data is used for compounds whose boiling points are below 250°C and ESI data for salts and high boiling point compounds.
A Mass Spec is measured by clicking on the Mass Spec machine and dragging the small sample tube to the solution of interest. The resulting Mass spectrum will be displayed in its own window with m/z on the x-axis. The height of the peaks give the relative abundance of each mass, and mousing over the peaks will give the exact m/z and relative height. Mass spectra of solutions containing mixtures are also allowed with the peaks adjusted for the relative concentrations. The OK button closes the Mass Spec window, and the Save button saves the Mass Spec to the lab book.
A spectra library containing over 700 spectra is available by clicking on the Spectra tab. When a Mass spectrum is obtained from the library, the IUPAC and common name for the compound and several physical properties are listed in the text boxes above the spectra. Spectra from the library can also be saved to the lab book. When a spectrum is generated from the lab bench, the text boxes are left empty since the spectrum is an unknown. The IUPAC and common name text boxes can be used to write notes about the spectra that will be attached to the spectra if saved.