8.2 b: Organic Analysis

​What we will cover:

• Why we use analytical techniques/organic spectrometry

• Summary of techniques

• Mass Spectroscopy

• NMR Spectroscopy

• Infrared (IR) spectroscopy

• UV Spectrophotometry

• Colourimetry
  

​Why do we use analytical techniques?

• Faster and more accurate analysis and identification of organic substances

• We combine these techniques to build a larger picture of a molecule

• We look at organic spectrometry techniques, and each of the instruments respond to a different energy input

​Summary of techniques:

​The electromagnetic spectrum (revision)

• Waves with a range of wavelengths and energies

• Spectroscopy relies on the full EM spectrum

​Mass Spectroscopy

• Note: specTROScopy is the study of the radiated energy, specTROmetry is the application of spectroscopy to assess results

• MS can give results on molar mass, elements present, and isotopes present

• Large variety of uses: on satellites, drug testing, radioactive dating

• Only needs a small sample for accurate results
  
  
  

​Components of a MS:

• Ionisation chamber - where particles are ionized into cations called molecular ions

• Pathway for particles - where they are accelerated by an electrical field. Then are separated by a magnetic field depending on their mass (m) and charge (z)

• Detector - where the separated ions are collected and their abundance can be determined

• Ionisation:

• The sample is vaporised into the gas phase by heating into the ionisation chamber where it comes in contact with high energy electrons that want to knock an electron off the sample molecule to turn it into a positively charged molecular ion - neutral molecules cannot be detected

• Usually only knock off 1 electron, so their charge is +1 (generally)

• The molecule is left with an unpaired electron, and it called a radical

• Only works if the molecule can be vaporised without decomposing - usually smaller organic molecules only

• Pathway:

• This is where acceleration and deflection occurs

• The charged particles are accelerated along the pathway by being attracted to negatively charged plates in the pathway. Their speed changes depending on their mass - lighter molecules move quicker

• The particles are then deflected by the magnetic field. This deflection changes depending n their mass (m) and charge (z). Smaller and lighter particles are easier to deflect

• Detection:

• The ions have different masses and charges, and will hit the detector at different times and speeds

• The computer hooked up to the MS then provides an output mass spectrum - which is a plot of mass/charge (m/z) vs abundance

• Only cations are detected by MS and therefore only cations show up on the spectrum plot

• Ions that are too big or too small will not be picked up and are removed from the MS viz vacuum

​Interpreting MS outputs:

• Plot produced is called a mass spectrum (ethanoic acid to the right)

• Because most molecules have a charge of 1, the x axis reading is really just the mass

• The most abundant peak is called the base peak, and is given a relative abundance of 100 - then every other molecule is plotted as a relative percentage of that peak

• Also can see the parent molecular ion, it will always be the largest mass

• To interpret we look at the fragmentation pattern

• The parent molecular ion peak is not the most abundant, this is because it has many different ways it can fragment

• When the double bond breaks it can make two different cations CH3+ and COOH+

• The COOH+ peak is much higher at 45, meaning that this fragmentation is much more common

• We can also look at the difference in peak values: i.e. is the parent peak is at 60, and there is another peak at 45, this difference of 15 indicates the loss of a methyl group, and the peak at 43 indicates a loss of 17 which corresponds to a hydroxyl group

​MS and Isotopes:

• We use MS to detect abundance of isotopes, because they differ in mass

• Can use it to determine the most abundant isotope in a sample and to calculate accurate average atomic mass

• Use this in carbon dating to determine the abundance of certain isotopes after radioactive decay over time - can determine the age of certain samples

​NMR Spectroscopy

• Nuclear magnetic resonance

• Study of the behaviour of nuclei when placed in a magnetic field

• Subatomic particles have a property called 'spin'

• Nuclei that have an odd atomic or mass number have a property called nuclear spin - ¹H and ¹³C for example

​NMR Spectrometer:

• The NMR spectrometer consists of a large magnet, a sample holder, a source of radio waves and a detector.

• The sample is placed into the magnetic field and will be irradiated with a range of different frequencies of radio waves.

• A number of these frequencies will be absorbed as particular nuclei flip.

• The detector records the energy waves emitted when the nuclear spin returns to the lower energy state.

• This produces NMR spectra that show series of lines correlating to the type and the environment of the nuclei.

​We use CDCl₃ as a solvent, as it does not have any H atoms - so therefore will not show up in the output

​How do we get data from NMR?

• Carbon atoms in bonds have electrons around them - these electrons cut down the size of the magnetic field they can feel

  • this is called shielding of the nucleus by electronegative atoms

• We get differing data because the carbon atoms are in different chemical environments - i.e. they have different things around them, so therefore a different frequency will be absorbed and then emitted

• This emission comes from when the nuclei release energy in the form of a radio wave when they flip back to their lower energy state

​What is a chemical environment?

• the energy required to flip a nucleus is dependent on the chemical environment it's in

​What is a chemical environment?

• the energy required to flip a nucleus is dependent on the chemical environment it's in

• a chemical environment differs when they are bonded to different things - meaning it will require different amounts of input energy to flip because of the different shielding capabilities of the atoms around it

• ethane has all H and C atoms in the same chem environment - so therefore, there would only be one spectrum line

• propanal has 3 different chem environments - so therefore will have 3 spectrum lines

​What is chemical shift?

• Chemical shift is the data we obtain from NMR measured in ppm, it is in comparison to a standard - this standard is tetramethylsilane (TMS)

• We use TMS because it is 4 carbon atoms in the same chemical environment and the carbon atoms are very shielded because the Si atoms are very close to them - this produces one very strong peak that sits always to the most left position

• the more polar a group is, the less shielded it is by its electrons, and therefore the more affected it will be by the radiowaves

• the more electronegative a neighboring atom is, the further downfield its chemical shift will be

You get given the NMR C data on your data sheet. If you need H data, it will be given to you!

We use this data when looking at NMR data output graphs


We use C-13 because it has an odd number of nucleons (protons + neutrons), so it can spin

​A. Because there is only 1 peak, there is only one H environment. Whereas B has 3, and C and D have 4.

​H NMR Interpretation

• Low resolution H NMR is the most common technique used. It's an abundant atom and in most organic molecules

• High resolution is what produces the splitting of the peaks (we will get to that)

• The number of peaks in the output is equal to the number of H environments

• The location of the peaks shows how shielded the H is

• To the right, there are 3 peaks and therefore 3 H environments

• The area underneath the peaks indicates the intensity, which is proportional to the amount of H's in that environment

​Go to Canvas if you want more info about integrator traces and peak intensity - it is slightly beyond the syllabus!

​High resolution H NMR - splitting

• The splitting of the peaks indicates how many protons/H+ are on adjacent atoms in this environment

• This is the n + 1 rule

  • The number of sub-peaks in a cluster is one more than the number of hydrogens attached to the next door carbon(s).

• We can make the assumption that there is only one carbon with hydrogens attached to the carbon we are interested in - we can make the assumptions to the right

Why does splitting occur?

• Due to spin spin coupling

• Spin-spin coupling is due to interactions between neighbouring non-similar protons

• The protons on the next-door carbon can be aligned with the H atom in the environment you're observing and provide shielding, or it is not aligned and deshields (and shifts the peak downfield)

• No splitting occurs when the two environments are the same, or when it has an OH group attached (there is no interaction between the H and the OH) - these will always appear as a singlet

​Example:

• ​Ethanol

• Has 3 H environments (a, b, c)

• a will have a triplet because it is next to the CH2 group

• b will have a quartet because it is next to the CH3 group

• c will have no splitting because there is no interaction between the H on the OH group and the H on the next-door carbon

​Example:

How many C environments are there?
Which one will correspond to which?

How many C environments are there?
- There are 2, because there are 2 distinct peaks

What will the molecule look like?
- see right

Which peak will correspond to which environment?
- right peak = the CH3, left peak = CH2Cl
- use data sheet

D. it has 2 C chemical environments

​Infrared Spectroscopy

• uses IR radiation to determine the bonds of functional groups present in a compound

• the IR radiation excites the bonds, and the bonds will vibrate and then stretch or bend either symmetrically or asymmetrically

• different functional groups absorb different IR frequencies, and this is what is measured

• very sensitive compared to other techniques in determination of functional groups

​What data is collected?

• the sample is placed in a small cell and then irradiated

• frequencies are absorbed by the sample

• the more energy that is absorbed, the less that makes it to the detector - the percentage that is transmitted to the detector is plotted against the frequency (100% transmittance means that no energy has been absorbed)

• we compare the values plotted against standard data and can determine the types of bonds - these are arranged by functional group

​How do we read the spectra outputs?

• (note: wavenumber is the inverse of wavelength)

• We often split it into two sections,

  • above 2000

    • usually has very few peaks

    • contains the CH bond around 3000 (which is in most if not all organic molecules) - just above indicates unsaturated, and just below indicates saturated

    • in 3000-3700 range you find peaks indicating bonds with exchangeable protons - usually belonging to alcohols, amines, amides, and carboxylic acids

  • below 2000

    • this is the main section we look at called the fingerprint region - because all functional groups have an identifiable peak in this region

​Example: ethanoic acid

• there is a ? next to C-O because it's in the fingerprint region, and we can't be sure it wasn't caused by something else

• however, OH bond at ~3000 is clear as OH acid

• C=O bond is clear

• can see the CH trough, but it's not useful for identification

• C-C is over a wise range so is also not useful