Mass Spectrometry Page

Introduction

Instrumentation

The Molecular Ion

Perhaps the most crucial piece of information obtained from the mass spectrum is the molecular mass of the compound in question. Structure elucidation requires knowledge of the chemical formula, and this can often be ascertained from the mass. The molecular ion (M+, that ion detected in mass spectrometry due to the loss of one electron from the molecule) provides the molecular mass of the compound directly. The sections below enumerate salient points to consider when interpreting EI mass spectra containing this important ion.

The Ionization Process

The Nitrogen Rule

Molecular Formula Determination

Accurate Mass

Isotope Ratio Data

Common Elements in Organic Compounds

Bromine and Chlorine

Fragmentation Patterns for Organic Functional Groups

Organic molecules will fragment in very specific ways depending upon what functional groups are present in the molecule. These fragments (if positively charged) are detected in mass spectrometry. The presence or absence of various mass peaks in the spectrum can be used to deduce the structure of the compound in question. We will study the major classes of organic functional groups and learn the ways in which these groups fragment. Once this material is mastered, a great deal of structural information from the mass spectrum can be deduced.

Alkanes

Straight Chain Alkanes

Branched Alkanes

Cyclic Alkanes

Unsaturated Hydrocarbons
Aromatic Compounds

Carbonyl Compounds

There are three important fragmentation pathways for carbonyl containing compounds: cleavage of bonds on either side of the carbonyl group (a-cleavage), cleavage of the a,b-bond (b-cleavage), and (if an alkyl chain of three carbons or more is attached to the carbonyl carbon) transfer of a g-hydrogen to the carbonyl oxygen followed by alkene elimination; this rearrangement is one of the few name reactions in mass spectrometry and is known as the McLafferty rearrangement. The most important fragment results from a-cleavage, as this process results in the formation of a resonance stabilized acylium ion.