# Structure Determination

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## Mass Spectrometry

Can be used to find the relative molecular mass, Mr, of a compound. Electrons in spectometer bombard sample molecules and break electrons off, forming ions with different mas-to-charge ratios. To find the Mr of a compound you look at the molecular ion peak, peak is due to the molecular ion, which is formed by the loss of an electron....     M^+. ----> X^+   +  Y^.   E.G molecular ion from butane: C4H10 ---> [C4H10]+     +  e-

The mass/charge value of the molecular ion peak is the molecular mass. For most organic compounds the M peak is the 2nd highest mass/charge ratio

M+1 Peak                                                                                                                                           The peak 1 unit to the right of the M peak is called the M+1 peak. Mostly due to the Carbon-13 Isotope, exists naturally. Can use the M+1 peak to work out how many carbon atoms there are in a molecule. : NUMBER OF CARBON ATOMS = ( HEIGHT OG M+1 PEAK/HEIGHT OF M PEAK) X 100.

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## Mass Spectrometry continued...

M+2 Peak                                                                                                                                               If the molecule has Cl or Br in it you will get a M+2 peak aswell as an M and a M+1 Peak. This is because Cl and Br have natural isotopes with different masses and they all show up on the spectrum.

COMPOUNDS CONTAINING Cl: Isotopes; Cl-35 and Cl-37, Ratio 3:1. So if a molecule has Cl in it will give an M peak and an M+2 peak with heights in the ratio 3:1.

COMPOUNDS CONTAINING Br: Isotopes; Br-79 and Br-81, Occur in equal amounts. So if a molecule contains Br, the M peak and M+2 peak will both have the same height.

If there is an M+4 peak, its because the molecule contains 2 atoms of the same halogen.

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## More Mass Spec

Fragmentation                                                                                                                                      In the mass spectrometer, bombarding of electrons make some of the molecular ions break into fragments. Fragments that are ions show up on the mass spectrum, making a fragmentation pattern. These patterns can be used to identify molecules and their structures.                                               To work out the structural formula, have to work out what ion could have made each peak from its m/z value. E.G:

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## Mass Spec- Fragment Stability

Some fragment ions are more stable than others so are more likely to form ---> more abundant, higher peaks on mass spectrum. 2 very stable fragment ions are Carbocations and acylium ions.

CARBOCATION STABILITY: Ion with a + charged carbon. They are relatively stable ions because alkyl groups feed electrons towards the + charge :

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Carbocations with more alkyl groups are more stable because more electrons are being donated to stabilise the carbocation

ACYLIUM ION STABILITY: (RCO+) often formed from aliphatic ketones. 2 possible structures of this ion, called resonance forms.

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## Mass Spec - Fragment Stability Cont.

More stable ions have higher peaks on the spectrum. Means the ions stabalised by resonance, like acylium ions, will have a higher abundance.

Good chance that a tall peak at m/z = 43 will be CH3CO+, and one thats m/z = 57 will be CH3CH2CO+.

Predicting Structures from Mass Spec

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## NMR

2 types: 13C NMR, gives info about how the C atoms in a molecule are arranged.                                      1H  NMR, tells you how the H atoms in a molecule are arranged.                                          Any atomic nucleus with an odd number of protons and neutrons has a nuclear spin. Causing it to have a weak magnetic field. NMR looks at how this magnetic field reacts when you put in a much larger external magnetic field..                                                                                                Hydrogen nuclei are single protons, have a spin whereas carbon has 6 P's and 6 N's, so no spin.

Effect of an external magnetic field

Normally nuclei are spinning in random directions --> magnetic fields cancel out. When a strong external magnetic field is applied, nuclei will align either with or opposed to the field. (one with the field are slightly lower energy level than the opposed nuclei)

Radio waves with the right frequency can give aligned WITH nuclei enough energy to flip to a higher energy level. nuclei that are OPPOSED to external field, can emit radio waves and flip down to a lower energy level.

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## NMR- Nuclear Environment and Chem Shift

Nuclear Environments                                                                                                                          A nucleus is partially sheilded from effects of external magnetic field by its surrounding electrons. Any other atoms or groups of atoms that are around the nucleus will also effect the amount of electron sheilding. So nucleus in a molecule fees different magetic fields depending on their environments. Meaning they absorb different amounts of energy at different frequencies.

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Chemical Shift                                                                                                                                      Nuclei in different environments absorb different frequencies. NMR spectroscopy measures these differences related to a standard substance --- difference is called chamical shift (   ). The Standard substance is tetramethylsilane (TMS):

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## NMR - TMS cont and 13C NMR

Has 12 H atoms all in identical environments and 4 C atoms all in identical environments. Meaning in 1H and 13C NMR it will produce a single absorption peak, well away from other peaks. Chemical shift is measured in parts per million (PPM) relative to TMS. so a single peak of TMS produced is given the chemical shift value of 0. Added to test sample for calibration purposes. It is inert, non-toxic and volatile (easy to remove).

13C NMR                                                                                                                                                If you have a sample of a chemical that contains carbon atoms, use 13C NMR spectrum of that molecule to help work out what it is. Spectrum will have one peak on it for each carbon environment in the molcule. Carbon atoms that are attracted to the more electronegative atoms will be less sheilded and so have a higher chemical shift.

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## NMR - Hydrogen Environments

Each peak on 1H NMR spectrum is due to one or more hydrogen nuclei in a particular environment.  Relative area under each peak tells you the relative number of H atoms in each environment.

Integration traces                                                                                                                                  1H NMR spectra can get cramped , not easy to see the ratios ---> so an integration trace is often shown. Height increases shown on the integration trace are proportional to the areas of the peaks

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## NMR- Chemical Shift and Splitting Patterns

Chemical Shift                                                                                                                                         Use a table (given in exam) to identify which functional group each peak in a 1H NMR spectrum is due to.  E.G:

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Splitting Patterns                                                                                                                                   Peaks on a 1H NMR spectrum may be split into smaller peaks (spin-spin splitting). N+1 Rule. SINGLET: 1 peak, 0 H's on adjacing C. DOUBLET: 2 peaks, 1 H on adjacent C. TRIPLET: 3 peaks, 2 H's on adjacent C. QUARTET: 4 peaks, 3 H's on adjacent C.

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## NMR- Proton-free solvents & Predicting structure

If a sample had to be dissolved, then a solvent is needed that does not contain any 1H atoms. Deuterated solvents are often used - Hydrogen atoms replaced by deuterium (D or 2H). It is a isotope of H that has 2 nucleons (a proton and a neutron) --> no nuclear spin, doesn't create a magnetic field. CCl4 can also be used.

Predicting structure from 1H NMR Spectra                                                                                            -Number of peaks, how many different H environments there are in the compound.                             -Ratio of peak areas, relative number of hydrogens in each environment                                              -Use chemical shift of each peak to work out what type of environment the H is in.                              -Splitting pattern of each peak tells you number of H's on adjacent carbon.     E.G. ...

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## Infrared Spectrometry

or IR, a beam of IR radiation is passed through a sample of a chemical. IR radiation is absorbed by covalent bonds in the molecues increasing their vibrational energy. Bonds between different atoms absorb different frequencies of IR radiation.

Infrared spectrometer produces a graph showing what frequencies of radiation the molecules are absorbing. You can use it to identify the functional groups in a molecule. Peaks show you where radiation is being absorbed.       E.G:

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## Chromatography Intro..

Used to seperate things in a mixture -- Once it is seperated out you can identify the components.

There are quite a few different types of chromatography, one need to know; Column chromatography and gas-liquid chromatography.

All types have 2 phases:

a MOBIE PHASE - Molecules can move, always liquid or gas.

a STATIONARY PHASE - Molecules cant move. Must be a solid.

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## Column Chromatography

Mostly used for purifying an organic product. Needs to be done to seperate it from unreacted chemicals or side products. Involves packing a glass column with a solid, absorbant material such as aluminium oxide coated with water -- called slurry. This is the stationary phase. Mixture to be seperated is added to the top of the column and allowed to drain through the slurry. A solvent is then run slowly and continually through the column, this is the mobile phase.

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As the mixture is washed through the column, components seperate out due to solubility in mobile phase and how strongly they are absorbed by stationary phase. Longer a component spends dissolved in a mobile phase, quicker it travels down the column. If a component spends a longer time absorbed onto stationary phase, longer take to travel down column. So more soluble a component in the mobile phase quicker pass through column.

As a component of mixture reaches the end of the column it is collected. Can then be identified using the time taken to move through column (retention time) or another technique (e.g. mass spec)

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## Gas-Liquid Chromatography

If you have a mixture of volitle liquids, use GLC to seperate them out so you can identify them.

Stationary phase is a viscous liquid, like oil, which coats the inside of a long tube. Tube coiled to save space, and it is built into an oven.                                                                                                Mobile phase is an unreactive carrier gas such as nitrogen. The sample is vaporised and passes through the oven as a gas.

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Each component takes a different amount of time to be injected into the tube to being recorded at the other end (retention time).

Retention time depends on how much time the component spends moving along with the carrier gas, and how much time it spends stuck to the viscous liquid. Each substance will have a different retention time---This can be used to identify the components of the mixture.

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