Determination of Structure

Mass Spectrometry Used to determine: the molar mass and the molecular formula. Structure of the molecule through fragmentation patterns.

Schematic of a mass spectrometer

Schematic of a mass spectrometer

How a mass spectrometer works When a sample is introduced into the machine the vaporized sample becomes ionized to form the molecular ion M+(g). Inside the machine this ion will break down into characteristic fragments which are also deflected by the magnetic field and which then show up as peaks on the detector. By looking at the difference in mass from the parent peak it is often possible to identify particular fragments.

Molar masses of common fragments Examples of some typical organic fragments that are made: (Mr -15)+ = loss of CH3 (Mr -29)+ = loss of C2H5 or CHO (Mr -31)+ = loss of CH3O (Mr -45)+ = loss of COOH

Mass spec. continued Reading a chart: Y axis: % intensity, or relative abundance The % of fragment present X axis:Mass to charge ratio (m/z) Gives the molar mass of the fragment.

Example chart from a mass spectrometer: determining a molar mass of a molecule

Mass spectrum of an organic molecule showing fragments produced. Ex Mass spectrum of an organic molecule showing fragments produced. Ex. propan-1-ol CH3-CH2-CH2-OH (M-29)+ CH2OH+ 100 31 80 Intensity % 60 (M-15)+ CH2 CH2OH+ C2H5+ M+ 40 29 45 60 20 20 40 60 80 Mass-to-charge (m/z) ratio

Mass Spectrum of propan-2-ol OH CH3-C-CH3 H (M-15)+ OH CH3C+ H 100 45 80 Intensity % 60 M+ 40 60 20 20 40 60 80 Mass-to-charge (m/z) ratio

Comparing the two charts. Both have the same M+ ion mass, indicating that they are isomers of C3H8O Propan-1-ol has its greatest peak at 31, a loss of 29. 31 is indicative of a -CH2OH fragment. The loss of 29 indicates a CH3CH2- fragment was formed. Propan-2-ol has its greatest peak at 45 at it contains two CH3- groups, which can fragment.

Propan-1-ol mass spectrum shows that there must be two carbons connected, an ethyl group. Therefore, the –OH must be on an end carbon. Propan-2-ol mass spectrum shows an abundance of CH3’s, methyl groups indicating the –OH must be on the middle carbon causing the two end carbons, methyl groups, to fragment.

Infrared Spectroscopy Can give the structural formula of certain functional groups Works on the principle: 1. all molecules vibrate, stretch and bend among the bonds 2. these differences in vibrations, bending etc, are due to the absorption of infrared light (IR) energy 3. each bond has a particular type of infrared that it absorbs. Thus, infrared absorption can indicate the bond present and, therefore, structure.

continued 4. The IR light absorbed is referred to by either its wavelength or more often by its frequency (f). So the wavelength or frequency is used to determine the structure.

A Simplified Correlation Chart (only a few of the possibilities) of wavelengths Bond Wavenumber/cm-1 C-O *1000-1300 C=C *1610-1680 C=O *1680-1750 C (triple line) C *2070-2250 O-H( in carboxylic acids) *2500-3300 C-H *2840-3095 O-H (in alcohols) *3230-3500

Infrared spectrum of a fingerprint on an aluminum slide Infrared spectrum of a fingerprint on an aluminum slide. The material was the explosive RDX.

Infrared reading of ethyl ethanoate

Interpreting an IR spectrum 1. Find the peaks on the spectrum 2. Read the wavelength correlating with the peak. 3. Use the infrared chart with wavelengths ranges to determine which functional group is responsible for the peak. 4. Use the functional groups to determine the category of the compound.

NMR Spectroscopy NMR spectroscopy gives information on the type of hydrogen atoms in a molecule. Specifically, -CH3, -CH2, CH2OH etc, The location of peaks and the height of the peaks indicate what type of hydrogen atoms and the number of hydrogen atoms, are present respectively.

How NMR works The nuclei of hydrogen atoms possess spin that exists in two different states of equal energy. When a radio frequency with a varying magnetic field is applied to a molecule, the hydrogen’s spin state align themselves either with or against the magnetic field. This alignment of the hydrogen absorbs energy. This energy comes from the absorption of radiation from the radio frequency being applied. This absorption, or chemical shift, makes a spectrum.

Why are there different absorption peaks? Each hydrogen does not absorb the same amount of radiation because they do not all have the same bond strength between itself and the carbon to which it is bonded. Bond strength is affected by surrounding bonds. Examples: CH3CH2CH3 There would be two peaks, or chemical shifts on its NMR spectrum indicating two different types of C-H bonds, CH3- and CH2- . The CH3- peak would be higher because there 6 of these H’s. There are only 2 of the other.

NMR spectroscopy Type of proton Chemical shift/ppm R-CH3 0.9 CH3COR(ester) 2.0 R-C-CH3 (Ketone) 2.1 R-OH 4.5 R-C-H (aldehyde) 9.7

Example: CH3CHCl2 There are 2 peaks, or chemical shifts, indicating 2 types of Hydrogen C-H bonds: CH3-, andCHCl2, The 2 peaks on this spectrum would not be similar in height, with the CH3- peak being higher with 3H’s the CHCl2 has only one H.

NMR spectrum of 1,1dichloroethane

How many peaks would there be in propane’s NMR spectrum? CH3CH2CH3

NMR spectrum for propane  CH3 CH2  C

Summary Chart Mass spectroscopy Infrared spectroscopy NMR Determines molar mass and branches Determines functional groups Determines the types of hydrogens present Uses electromag. Uses infrared radiation Uses radiowaves Chart has: Y=%abundance X=mass Y=%transmissi X=wavelength Y=#of protons X=chem.shift/

Summary continued No single test is adequate in determining the structure of a molecule. The tests are effective when combined with each other. The best way to identify an unknown molecule is to compare its tests results with a known molecule.