Analytical Chemistry

Question 1

What is solvent extraction?

Answer 1

A separation funnel is used to separate 2 layers of immiscible liquids. This involves an aqueous phase (hydrophilic) and an organic phase (hydrophobic).

Question 2

What is the distribution ratio, Kd?

Answer 2

A quantitative measure for the affinity of a chemical compound to partition in each phase.

Question 3

What does it mean if Kd<1?

Answer 3

The compound will preferentially partition into the organic phase.

Question 4

How is effective separations achieved?

Answer 4

By repeating the separation several (usually 3) times and combining the fractions.

Question 5

What is chromatography and what are the 2 phases?

Answer 5

A technique based on the distribution of the analytes between 2 immiscible phases. The stationary phase is filled into the column and has some property that effects separation based on the physical characteristics we are looking at. The mobile phase is what passes through the column and contains the substances we want to separate.

Question 6

What is liquid-liquid chromatography?

Answer 6

Both phases are liquid (one organic and one aqueous). The stationary phase is immobilised in a column and the mobile phase passes through. This process is called elution and analytes with different affinities will elute at different times. Analytes with higher affinities for the mobile phase will elute earlier. Different analytes have different retention times which can be used to identify a given sample.

Question 7

What is size-exclusion chromatography?

Answer 7

Mainly used to separate biological macromolecules. Uses beads with holes of defined sizes as stationary phase. Small molecules which fit the holes will stay on the column for longer and have larger retention times than larger analytes.

Question 8

What is separation based on charge?

Answer 8

Charged analytes can be separated by either anion or cation exchange chromatography. The mobile phase includes a mixture of anions and cations. Anions are immobilised on the stationary phase and cations in the mobile phase will be attracted so are retained in the column. Anions in the mobile phase will pass straight through.

Question 9

What is separation based on affinity?

Answer 9

Affinity chromatography is based on specific interaction of the analytes in the mobile phase with antibodies immobilised on the stationary phase. The antibodies specifically recognise and bind to a particular analyte.

Question 10

What is gas chromatography?

Answer 10

A technique for volatile analytes. The mobile phase is an inert carrier gas and the stationary phase is usually a liquid but sometimes a solid.

Question 11

What is reversed phase high performance liquid chromatography (HPLC)?

Answer 11

Able to separate analytes with subtle differences in physical properties including structural isomers and diastereoisomers.

Question 12

What is electrophoresis used for?

Answer 12

To separate charged macromolecules through a combination of charge, size and shape.

Question 13

What is the electrophoresis gel made of and what is added to it?

Answer 13

The gel is made of polyacrylamide and the anionic surfactant sodium dodecylsulfate is added to it to form SDS-PAGE.

Question 14

What are the steps in electrophoresis?

Answer 14

1. The sample is loaded to the top of the SDS-polyacrylamide.
2. An electrical current is then applied which drags the charged molecules within the sample through the gel.
3. A marker is used to show when the sample has travelled the length of the gel.
   Large molecules move slowly and small molecules move more quickly.

Question 15

What is isoelectric focussing (IEF)?

Answer 15

Separates proteins using a gel containing a pH gradient. Each protein will move through the gel until its isoelectric point is reached.

Question 16

What is the isoelectric point of a protein?

Answer 16

The pH at which there is no net charge.

Question 17

What is 2D gel electrophoresis?

Answer 17

Proteins are separated by IEF and then the gel is coated by 90 degrees and subjected to SDS-PAGE. This allows complex protein mixtures to be separates into individual proteins.

Question 18

What does DNA profiling make use of?

Answer 18

Makes use of short tandem repeats, and short identical non-coding DNA sequences (the number of which are different between individuals).

Question 19

What does sedimentation mean?

Answer 19

The process of molecules sinking through a liquid medium when subjected to a force (e.g. gravity).

Question 20

What is centrifugation?

Answer 20

When sedimentation is sped up by applying a centrifugal force through spinning it in a centrifuge. Centrifuges must always be balanced by weighing the vials. Centrifugation gives he solid matter as a pellet and the liquid is the supernatant.

Question 21

What are the 4 categories of centrifugation?

Answer 21

1. Benchtop low-speed.
2. Benchtop microfuges.
3. High-speed floor-standing.
4. Ultracentrifuges

Question 22

What is density gradient centrifugation?

Answer 22

Where several layers of varying density are used and different components of the sample will accumulate at the boundaries of the different layers according to their density.

Question 23

What is mass spectrometry?

Answer 23

A separation technique which relies on ionisation and mass separation of molecules. Can be used to measure mass-to-charge ratios (m/z) of molecules and their ion fragments. Does mot rely on absorption or emission of electromagnetic radiation.

Question 24

Can MS distinguish between structural isomers? Why?

Answer 24

No because they have the same mass.

Question 25

What is the principle of a mass spectrometer?

Answer 25

1. Analyte is vaporised and ionised. Resulting ions are deflected in an electromagnetic field/MS.
2. Vapour/gaseous sample is loaded.
3. Ionization chamber generates ions from the gaseous sample.
4. Analyser separates ions.
5. Ion detector detects ions.

Question 26

What is the traditional mass spectrometer?

Answer 26

1. A particle is accelerated along a straight path.
2. A force is applied to deflect the particle from its path.
3. A detector detects the deflected particle.

By gradually changing the field strength we can determine the mass of the ions reacting the detect (m/z).

Question 27

What are 2 examples of modern mass spectrometers?

Answer 27

1. Time-of-flight (TOF) - Ion is accelerated before being allowed to drift to the detector. Time taken to drift depends on the ions momentum (therefore mass).
2. Quadrupole - Sample enters analyser, the path is disrupted by the electrical field and at a given current only ions of a certain mass have a stable trajectory and reach the detector.

Question 28

What is the base peak (MS)?

Answer 28

The most intense ion of the mass spectrum. All other peaks are reported relative to the base peak on the y-axis.

Question 29

What is electron impact (EI) MS?

Answer 29

A beam of high energy electrons knocks out one electron from the analyte, resulting in a radical with one positive charge (molecular ion).

Question 30

What happens in electrospray (ESI) MS?

Answer 30

Ionisation is achieved by transferring one (or more) protons onto the molecule to give a quasimolecular ion. For large proteins, different quasimolecular ions are observed simultaneously all indicating the same molecular weight.

Question 31

What is deconvolution?

Answer 31

Determining the charge state (z).

Question 32

What is MS-MS (tandem mass spectrometry)?

Answer 32

Ions generated in one mass spectrometer are inserted into a second MS and fragmented into smaller pieces. Proteins can be separated using this technique.

Question 33

What is wave/particle duality?

Answer 33

The idea that electromagnetic radiation can be regarded as both waves and particles.

Question 34

What is absorption and emission spectroscopy process?

Answer 34

Involves the transitions from a lower energy ground state to one or more higher energy excited states and vice versa. Energies are quantised (only discrete energy levels are allowed). Both absorption and emission can be measured. Only electromagnetic radiation of the correct energy will intact with the molecule, the rest will pass through unchanged.

Question 35

What is an absorption spectrum and what is a transmission spectrum,?

Answer 35

Absorption - measures the amount of radiation being absorbed by the sample.
Transmission - Measures the amount of radiation being transmitted through the sample (passing through/not being absorbed).

Question 36

What is NMR spectroscopy?

Answer 36

Based on the absorption of radio waves by certain nuclei when placed in a strong magnetic field. Most powerful spectroscopic technique used for structure explanation of small molecules. 1H NMR spectra contains chemical shifts, coupling patterns and integrals. The most important information in 13C NMR spectra are chemical shifts.

Question 37

Describe what happens to 1H and 13C nuclei in an external magnetic field.

Answer 37

They behave like bar magnets and align themselves with regard to the direction of the field. 2 orientations possible - aligned with (lower energy state) or aligned against the external magnetic field (higher energy state). Absorption of suitable radio wave-range radiation leads to a spin-flip of the nuclei, while the energy released when returning to the ground state yields the NMR signal.

Question 38

How is the nucleus ‘shielded’ from the external magnetic field in NMR?

Answer 38

Because they are surrounded by electrons which produce their own magnetic field that is opposed to the external magnetic field. Differences in number and distribution of electrons depending on bonding and structure will make the signals appear at different chemicals shifts (expressed in ppm, relative to TMS).

Question 39

What is tetramethylsilane (TMS)?

Answer 39

Assigned a chemical shift of 0. All chemical shifts are expressed relative to TMS.

Question 40

What is the chemical shift of a peak?

Answer 40

The difference between the resonance frequency of the compound being studied and the resonance frequency of TMS. It reflects the chemical environment of a given nucleus. Electron-withdrawing substituents such as oxygen reduce the electron-density around a nucleus, leading to a higher chemical shift. The absence of electron-withdrawing substituents makes a nucleus more electron-rich leading to a lower chemical shift.

Question 41

Why does the 13C NMR spectrum only show 2 signals for propane?

Answer 41

Because the 2 methyl groups are in the same chemical environment, making the peak of the methyl signal quite intense (but peak heights have no reliable physical meaning in 13C NMR).

Question 42

Describe 1H NMR spectroscopy.

Answer 42

Each group of chemically equivalent protons gives one signal. The chemical shift reflects the chemical environment of a given nucleus. The relative number of protons that contribute to a given signal can be concluded from its integral (not peak height).

Question 43

What happens in an MRI scan?

Answer 43

We measure a 1H NMR spectrum of a patient. The image is derived mainly from water which occurs in different amounts in soft tissues. Functional MRI (fMRI) images blood flow in the brain and displays regions of the brain which are active during cognitive processes.

Question 44

What is the effect of infrared electromagnetic radiation on bonds?

Answer 44

It causes them to vibrate. Functional groups have characteristic vibrational frequencies which can be used to identify them. (IR main application is to identify functional groups).

Question 45

Which terms are used to describe the bond vibrations (5)?

Answer 45

Stretch, scissor, rock, wag and twist.

Question 46

What are the 2 factors that influence how fast a bond vibrates?

Answer 46

1. Strength of the bond - high energy (stronger) bonds vibrate more quickly (e.g. C=C) than weaker, lower energy bonds (e.g. C-C).
2. The reduced mass - As the mass increases, the vibration speed decreases.

Question 47

How is IR spectra displayed?

Answer 47

As a transmission spectra. If the infrared light is not of the right wavelength to be absorbed by the molecule, it is transmitted by the molecule and strikes the detector. If it is of the right wavelength, it is absorbed and so does not reach the detector. The % transmittance is printed as a function of the wavenumber decreasing from left to right.

Question 48

How can we determine functional groups of organic compounds from an IR spectra?

Answer 48

Each functional group will give a characteristic peak in the spectrum. Both the presence and absence of a certain band can be diagnostic. In general, stretching vibrations require more energy than bending vibrations but are more characteristic.