Structure Determination

Structure Determination

1. Mass Spectrometry

   • Fragmentation
     • If a molecular ion ( a radical cation), breaks up, one fragment will carry a positive charge and the other an unpaired electron
       • Only the charged fragment (+) will be detected
     • Fragmentation is more likely to take place at weaker bonds
     • The more stable the fragment that forms the greater its abundance in the spectrum
     • The stability of positive ions formed from hydrocarbons (carbocation) is in the order tertiary>secondary>primary
   • Fragmentation of Carbonyl Compounds
     • A carbonyl compound will typically fragment at the carbonyl group to give an alkyl radical and a stable RCO+ cation, called an acylium ion
       • This is stable because the RCO+ ion has a positive charge localised on the carbon atom and the carbonyl group is polarised because oxygen is more electronegative
   • Measuring Relative Molecular Mass- The molecular ion
     • Since most ions formed have lost a single electron, they have an unpaired electron and are also free radicals
       • These are called radical cations
     • The peak furthest to the right of the mass spectrum corresponds to the molecular ion
       • Molecules containing isotopes will produce more than one molecular ion

2. Intra-red (IR) Spectrometry

   • Infra-red Spectra of Alcohols
     • The O-H vibration is called a stretch
       • The large range of values is caused by hydrogen bonding between alcohol molecules
         • Each vibration hydrogen will be bonded to a varying number of other alcohol molecules, which will tend to slow down the vibration
   • Infra-red Spectra of C=O group
   • The Fingerprint region
     • The area of an IR spectrum below about 1500cm-1 usually has many peaks, caused by the vibrations of the molecule as a whole
       • The shape of the region is unique for any particular substance
   • Identifying groups of atoms
     • Particular functional groups produce peaks in different areas of the spectrum
       • The frequencies of peaks are called the wavenumbers and are measured in the units, cm-1
     • IR can be used to spot the presence of impurities by comparing the IR spectrum of a pure sample with the IR spectrum of the sample that may have impurities
       • Impurities will cause peaks to appear in the infra red spectrum which cannot appear with a pure sample

3. Nuclear Magnetic Resonance Spectrometry

   • Carbon-13 nmr
     • Chemical shift is measured in parts per million (ppm) from a defined 0 related to a compound called TMS (Tetramethylsilane)
       • In 13C nmr values range from 0 to around 200 ppm
         • Carbon atoms in different environments will give different chemical shift values
   • Proton nmr
     • In proton nmr, it is the H1 nucleus being examined
       • Nearly all hydrogen atoms are H1 so it is easier to get an nmr spectrum for 1H than 13C
         • Hydrogen atoms in different environments will give different chemical shift values
           • The values of chemical shift in proton nmr range between 0 and 10 ppm
     • Tetramethylsilane
       • TMS (Si(CH3)4) is the standard that chemical shift values are measured in reference to
         • The chemical shift value of these hydrogen atoms is zero by definition
         • A small amount is added to the sample to calibrate the system
           • TMS is used because it is inert, it is non-toxic and it is easy to remove from the sample
     • Integration value of each signal is proportional to the number of equivalent H atoms it represents
     • Spin-Spin Coupling
       • Spin-spin coupling is the splitting of nmr peaks into particular patterns depending on the neighbouring hydrogen atoms
         • The rule is: n hydrogen's on an adjacent carbon atom will split a peak into n+1 smaller peaks
     • Solvents from 1H nmr
       • nmr spectra are normally run in solution but the solvent must not contain any hydrogen atoms as they would hide the chemical shift values of the sample and so tetrachloromethane (CCl4) is used

4. Chromatography

   • In chromatography a sample can be separated if it is dissolved in a solvent and then the resulting solution (mobile phase) moves over a solid (stationary phase)
     • The mobile phase (eluent) carries the soluble components of the mixture with it. The more soluble the mixture in the mobile phase the faster it moves
     • The stationary phase will hold back the components in the mixture that are attracted to it. The more affinity a component has for the stationary phase the slower it moves with the solvent
       • Every compound of the mixture has a unique balance between its affinity for the stationary and for the mobile phase
   • Column Chromatography
     • Column chromatography uses a powder such as silica as the stationary phase.
       • This is packed into a narrow tube- the column- and a solvent (the eluent) is added to the top
         • As the eluent runs down the column, the components of the mixture move at a different rate and can be collected separately in a flask at the bottom
   • Gas-Liquid Chromotography
     • The stationary phase is a powder coated with oil
       • This is either packed into or coated onto a long capillary tube.
         • The mobile phase is usually an unreactive gas, such as nitrogen
           • After injection, the sample is carried along by the gas and the mixture separates as some of the components move along with the gas and some are retained by the oil, each to a different degree
             • This means that the components leave the column at different times after injection- they have different retention times

Images and files in the map