Lecture 14 Monday February 9 2015 1 39 PM Mass spectroscopy Mass spec gives us a spectrum with X axis showing m z m mass z charge and y axis being abundance So it shows abundance of charged species of a particular mass to charge ratio In general z is 1 as the most abundant charged species at least in the analysis of small organic molecules are single charged ions cations and anions With large biomolecules polyions are common Overall the X axis is more or less equal to a mass of the ion The large highest mas peaks 106 in the 1 and 121 in the second spectrum are peaks of the actual molecule and we call them molecular peak the smaller peaks 91 in the first and 105 77 in the second are peaks of the smaller fragments that are produced when the molecule falls apart How and why this happens and how do we get spectrum This is a scheme of a mass spectrometer We introduce a sample and that sample is vaporized and hit by accelerated electrons The kinetic energy of the impact is sufficient to cause ionization of the sample molecule and leaves enough energy in a molecule that it causes breaking of the bonds in the molecule That s why we get a ionized molecule and the fragments Ions are then accelerated in the electric field and focused through a slit 4 When ions pass through the magnetic field the field induces circular electric current and ions start going along a circular trajectory However the ions exit the magnetic field and the continue going at the tangent The trajectory is going to be determined by how much magnetic field was able to influence the ions that depends on their inertia mass and they charge So depending on the mass charge ratio the ions are going to be distributed in space and fall at the different place on the detector We use that to obtain mass charge ratio of the ions present in the sample For export Page 1 Lecture 14 Monday February 9 2015 1 39 PM Few words about fragmentation Generally abundance of fragments corresponds to the stability of the carbocations That s why the most abundant peak in the first spectrum corresponds to the benzyl cation Fragmentation can be useful in determining the structure of the unknown compounds however sometimes it can prevent us from seeing a molecular peak and obtaining a mass molecular weight and molecular formula of a molecule That s why we developed a range of methods for ionization of the sample Ionization methods 1 Hard methods produce many fragments and often do not give molecular ion electron impact fast electrons cause ionization of the sample in the gas phase 2 Soft ionization produces molecular ion as the major ion and few if any fragemnts Examples Electron spray High electrical field causes ionization in the process very little extra energy is transferred to the molecule Fast atom bombardment FAB Fast atoms are used to cause ionization and desorption of molecules from a liquid matrix solution MALDI matrix assisted laser desorption ionization As it says laser transfer energy to a solid matrix that transfers it to a sample molecule and causes desorption molecules go to a gas phase and ionization Excellent for large and sensitive biomolecules Peaks with smaller weight correspond to the fragments What about the smaller peaks around a molecular peak that have a bigger weight Those come from higher mass isotopes Most carbons are 12C but 1 1 are 13C Similar situation is with other heteroatoms such as N and O Small abundance of higher weight isotopes Givent that those abundances are different form each atom we can use those small peaks and their abundances to determine molecular formulas in those situation where exact masses are similar For example C2HN3O and C2H3N4 have very similar masses but quite different isotope abundances and we can use that to determine the correct molecular formula Some atoms have very diagnostic isotope pattern Br has two isotopes Br79 and Br81 that are present in roughly equal amount So when there are peaks that are 2 m z units apart in the same ratio we can tell that there is bromine in the molecule Similarly Cl35 is 3X more common than Cl37 Information we can get from mass spec We can get 1 2 3 Exact mass molecular weight and molecular formula Isotope content and ratio of isotopes Structural information from fragmentation pattern powerful when coupled with libraries of spectra of known compounds For export Page 2 Lecture 14 Monday February 9 2015 1 39 PM NMR numbers and environment of H and C in a molecule IR presence or absence of functional groups in a molecule UV Vis presence or absence of a conjugated system Mass Spectrometry MW determination molecular formula Organometallic compounds Properties M always have lower electronegativity than C So bond is always polarized in a way that C is partially negatively charged For export Page 3 Lecture 14 Monday February 9 2015 1 40 PM Preparation Order of reactivity Mechanism This is an energy diagram for R X radical anion Putting electrons into a sigma star anti bonding orbital weakens the R X bond That s why R X radical anion which has one electron in the sigma star dissociates into the radical and halide anion Mechanism is the same for Mg A simpler and more commonly used method for synthesis of alkyl lithium reagents relies on the equilibrium between the organometallic reagents and alkyl halides The position of the equilibrium depends on the stability of organolithium reagents By using the least stable tert butyl lithium we can ensure that the equilibrium will favor the formation of the R Li we want Tertiary carbanions are less stable than 1 2 aryl or vinyl anion Using tertbutyl lithium we can make all of these organolithium reagents For export Page 4