Mass spectral interpretation is the method employed to identify the chemical formula, characteristic fragment patterns and possible fragment ions from the mass spectra. Mass spectra is a plot of relative abundance against mass-to-charge ratio. It is commonly used for the identification of organic compounds from electron ionization mass spectrometry. Organic chemists obtain mass spectra of chemical compounds as part of structure elucidation and the analysis is part of many organic chemistry curricula.
Mass spectra generation
Electron ionization (EI) is a type of mass spectrometer ion source in which a beam of electrons interacts with a gas phase molecule M to form an ion according to
M + e − → M + ∙ + 2 e − {\displaystyle M+e^{-}\to M^{+\bullet }+2e^{-}}
with a molecular ion M + ∙ {\displaystyle M^{+\bullet }} . The superscript "+" indicates the ion charge and the superscript "•" indicates an unpaired electron of the radical ion. The energy of the electron beam is typically 70 electronvolts and the ionization process typically produces extensive fragmentation of the chemical bonds of the molecule. Due to the high vacuum pressure in the ionization chamber, the mean free path of molecules are varying from 10 cm to 1 km and then the fragmentations are unimolecular processes. Once the fragmentation is initiated, the electron is first excited from the site with the lowest ionization energy. Since the order of the electron energy is non-bonding electrons > pi bond electrons > sigma bond electrons, the order of ionization preference is non-bonding electrons > pi bond electrons > sigma bond electrons.
The peak in the mass spectrum with the greatest intensity is called the base peak. The peak corresponding to the molecular ion is often, but not always, the base peak. Identification of the molecular ion can be difficult. Examining organic compounds, the relative intensity of the molecular ion peak diminishes with branching and with increasing mass in a homologous series. In the spectrum for toluene for example, the molecular ion peak is located at 92 m/z corresponding to its molecular mass. Molecular ion peaks are also often preceded by an M-1 or M-2 peak resulting from loss of a hydrogen radical or dihydrogen, respectively. Here, M refers to the molecular mass of the compound. In the spectrum for toluene, a hydrogen radical (proton-electron pair) is lost, forming the M-1 (91) peak. Peaks with mass less than the molecular ion are the result of fragmentation of the molecule. Many reaction pathways exist for fragmentation, but only newly formed cations will show up in the mass spectrum, not radical fragments or neutral fragments. Metastable peaks are broad peaks with low intensity at non-integer mass values. These peaks result from ions with lifetimes shorter than the time needed to traverse the distance between ionization chamber and the detector.
Molecular formula determination
Nitrogen rule The nitrogen rule states that organic molecules that contain hydrogen, carbon, nitrogen, oxygen, silicon, phosphorus, sulfur, or the halogens have an odd nominal mass if they have an odd number of nitrogen atoms or an even mass if they have an even number of nitrogen atoms are present. The nitrogen rule is true for structures in which all of the atoms in the molecule have a number of covalent bonds equal to their standard valency, counting each sigma bond and pi bond as a separate covalent bond.
Rings rule From degree of unsaturation principles, molecules containing only carbon, hydrogen, halogens, nitrogen, and oxygen follow the formula
Rings + π -Bonds = u = C − H 2 − X 2 + N 2 + 1 {\displaystyle {\text{Rings}}+\pi {\text{-Bonds}}=u=C-{\frac {H}{2}}-{\frac {X}{2}}+{\frac {N}{2}}+1\,}
where C is the number of carbons, H is the number of hydrogens, X is the number of halogens, and N is the number of nitrogen.
Even electron rule The even electron rule states that ions with an even number of electrons (cations but not radical ions) tend to form even-electron fragment ions and odd-electron ions (radical ions) form odd-electron ions or even-electron ions. Even-electron species tend to fragment to another even-electron cation and a neutral molecule rather than two odd-electron species.
Stevenson's rules The more stable the product cation, the more abundant the corresponding decomposition process. Several theories can be utilized to predict the fragmentation process, such as the electron octet rule, the resonance stabilization and hyperconjugation and so on.
Rule of 13 The Rule of 13 is a simple procedure for tabulating possible chemical formula for a given molecular mass. The first step in applying the rule is to assume that only carbon and hydrogen are present in the molecule and that the molecule comprises some number of CH "units" each of which has a nominal mass of 13. If the molecular weight of the molecule in question is M, the number of possible CH units is n and
M 13 = n + r 13 {\displaystyle {\frac {M}{13}}=n+{\frac {r}{13}}\,}
where r is the remainder. The base formula for the molecule is
C n H n + r {\displaystyle C_{n}H_{n+r}\,}
and the degree of unsaturation is
… excerpt ends here. Continue reading the full article.
