If you're seeing this message, it means we're having trouble loading external resources on our website.

If you're behind a web filter, please make sure that the domains *.kastatic.org and *.kasandbox.org are unblocked.

Main content

Principles of chromatography

‘Chromatography’ is an analytical technique commonly used for separating a mixture of chemical substances into its individual components, so that the individual components can be thoroughly analyzed. There are many types of chromatography e.g., liquid chromatography, gas chromatography, ion-exchange chromatography, affinity chromatography, but all of these employ the same basic principles.
Chromatography is a separation technique that every organic chemist and biochemist is familiar with. I, myself, being an organic chemist, have routinely carried out chromatographic separations of a variety of mixture of compounds in the lab. In fact, I was leafing through my research slides and came across a pictorial representation of an actual chromatographic separation that I had carried out in the lab. I guess that picture would be a good starting point for this tutorial!
Let me first explain what I was trying to do here. I had two reactants ‘A’ and ‘B’. I let them react with each other, under certain reaction conditions, to form a product ‘C’. After the reaction was complete, I ended up with a reaction mixture that contained unreacted A, unreacted B and my desired product C. Now my task was to separate out A, B and C to isolate and analyze pure product C.
First, as shown in the left hand side panel, I ran a thin layer chromatography (TLC) plate. This is basically a rectangular piece of glass plate, coated with a thin layer of silica. I applied a spot of the reaction mixture just above the base of the plate (denoted with a solid line), and placed the plate in a jar that contained an appropriate organic solvent (in this case, 1:1 volume by volume mixture of hexane:ethyl acetate was used), with just enough volume to dip the lower edge of the plate. Gradually by capillary action, the solvent started rising up the silica plate, and as you can see the reaction mixture separated into 3 spots with distinct colors by the time the solvent had reached the solvent front mark.
Next, in order to actually perform the separation, I assembled a glass column (as shown on the right hand side of the picture). I took a glass column with a stopcock attached at the bottom, inserted a cotton plug at the bottom of the column and packed the column with a slurry of silica gel (prepared in an organic solvent). Once the column was packed, and the solvent volume above the bed reduced to less than 5 mm, I carefully poured the reaction mixture over the bed of silica from the top of the column, with the aid of a glass pipette. I opened the stopcock and let the solvent run slowly through the column. I constantly kept adding solvent from the top of the glass column. As you can see, the reaction mixture started separating into three distinct bands - yellow, pink and orange corresponding to unreacted B, unreacted A and the desired product C, respectively. I collected individual bands in separate flasks and was thus able to obtain pure C!

Principles of chromatography

Let’s first familiarize ourselves with some terms that are commonly used in the context of chromatography:
Mobile phase or carriersolvent moving through the column
Stationary phase or adsorbentsubstance that stays fixed inside the column
Eluentfluid entering the column
Eluatefluid exiting the column (that is collected in flasks)
Elutionthe process of washing out a compound through a column using a suitable solvent
Analytemixture whose individual components have to be separated and analyzed
Now let’s try to understand the principle of chromatography. Let us draw a pictorial representation of a column chromatographic separation set up.
As depicted above, the analyte is loaded over the silica bed (packed in the column) and allowed to adhere to the silica. Here, silica acts as the stationary phase. Solvent (mobile phase) is then made to flow through the silica bed (under gravity or pressure). The different components of the analyte exhibit varying degrees of adhesion to the silica (see later), and as a result they travel at different speeds through the stationary phase as the solvent flows through it, indicated by the separation of the different bands. The components that adhere more strongly to the stationary phase travel more slowly compared to those with a weaker adhesion. Analytical chromatography can be used to purify compounds ranging from milligram to gram scale.
Before we move on, let’s conduct a simple experiment to exemplify the power of a chromatographic separation.
  1. Take a few leaves and crush them in a mortar.
  2. Spot a drop of the leaf extract on a strip of chromatographic paper ~ 0.5 cm above the edge of the paper. Chromatographic paper is made of cellulose and is quite polar in nature.
  3. Place the strip of paper in a jar that contains a small volume of propanone (acetone). There should be just enough propanone that the edge of the paper dips in it comfortably. Place a lid on the jar to avoid any evaporation of the solvent.
  4. Let the solvent rise up the paper by capillary action. Remove the paper strip from the jar once the solvent has reached the ‘solvent front’ level. 5) What do you think you will notice?
The various components of the leaf pigment separate out! Could you have ever imagined that a leaf pigment was made up of so many compounds?
Principle of separation of different components: Differential affinities (strength of adhesion) of the various components of the analyte towards the stationary and mobile phase results in the differential separation of the components. Affinity, in turn, is dictated by two properties of the molecule: ‘Adsorption’ and ‘Solubility’.
We can define adsorption as the property of how well a component of the mixture sticks to the stationary phase, while solubility is the property of how well a component of the mixture dissolves in the mobile phase.
  • Higher the adsorption to the stationary phase, the slower the molecule will move through the column.
  • Higher the solubility in the mobile phase, the faster the molecule will move through the column.
So, the interplay between the above two factors determines the differential rates at which the different components of the analyte will move through the column. Adsorption and solubility of a molecule can be manipulated by choosing the appropriate stationary phase and mobile phase.
Now, the question arises why do different compounds possess different affinities towards the stationary and mobile phases? “Polarity” of the compounds dictates their affinities towards the stationary and mobile phases. Let’s understand this through an example.
Suppose we have a mixture of two molecules A and B, where ‘A’ is a protein and ‘B’ is a lipid. Our column is packed with silica, which is polar in nature; our mobile phase is hexane, which is non-polar in nature. What do you think will happen when we load this mixture of A and B onto this column?
‘A’, being polar in nature, will adsorb on to the polar stationary phase (silica). ‘B’ being non-polar in nature, will readily dissolve in the non-polar mobile phase (hexane) without adhering to silica, and will thus elute out of the column with hexane. Once B is eluted out, the mobile phase will be changed to something polar like acetonitrile. By doing so we will now force A to detach from the silica and dissolve in the polar solvent, acetonitrile, and get eluted out of the column with acetonitrile. This is illustrated in the diagram below.

Different types of chromatography

Throughout this article we are dealing with what we refer to as normal-phase chromatography, implying that our stationary phase is polar (hydrophilic) in nature and our mobile phase is non-polar (hydrophobic) in nature. For special applications, scientists sometimes employ reverse-phase chromatographic techniques where the scenario is reversed i.e. the stationary phase is non-polar while the mobile phase is polar.
There are several types of chromatography, each differing in the kind of stationary and mobile phase they use. The underlying principle though remains the same: differential affinities of the various components of the analyte towards the stationary and mobile phases results in the differential separation of the components. Again, the mode of interaction of the various components with the stationary and mobile phases may change depending on the chromatographic technique used. The commonly used chromatographic techniques are tabulated below.
TechniqueStationary phaseMobile phaseBasis of separationNotes
*Paper chromatographysolid (cellulose)liquidpolarity of moleculescompound spotted directly on a cellulose paper
*Thin layer chromatography (TLC)solid (silica or alumina)liquidpolarity of moleculesglass is coated with thin layer of silica on which is spotted the compound
*Liquid column chromatographysolid (silica or alumina)liquidpolarity of moleculesglass column is packed with slurry of silica
Size exclusion chromatographysolid (microporous beads of silica)liquidsize of moleculessmall molecules get trapped in the pores of the stationary phase, while large molecules flow through the gaps between the beads and have very small retention times. So larger molecules come out first. In this type of chromatography there isn’t any interaction, physical or chemical, between the analyte and the stationary phase.
Ion-exchange chromatographysolid (cationic or anionic resin)liquidionic charge of the moleculesmolecules possessing the opposite charge as the resin will bind tightly to the resin, and molecules having the same charge as the resin will flow through the column and elute out first.
Affinity chromatographysolid (agarose or porous glass beads on to which are immobilized molecules like enzymes and antibodies)liquidbinding affinity of the analyte molecule to the molecule immobilized on the stationary phaseif the molecule is a substrate for the enzyme, it will bind tightly to the enzyme and the unbound analytes will pass through in the mobile phase, and elute out of the column, leaving the substrate bound to the enzyme, which can then be detached from the stationary phase and eluted out of the column with an appropriate solvent.
Gas chromatographyliquid or solid supportgas (inert gas like argon or helium)boiling point of the moleculessamples are volatilized and the molecule with lowest boiling point comes out of the column first. The molecule with the highest boiling point comes out of the column last.
*Fall under the category of ‘Liquid Chromatography’

Thin layer chromatography (TLC): Retention factors (Rf)

Just to refresh our memories, normal phase thin layer chromatography is performed on a piece of glass plate that is coated with a thin layer of silica. Here, silica acts as the stationary phase and the solvent in which the plate is dipped and that runs up the plate by capillary action is the mobile phase. The stationary phase i.e. silica is very polar in nature, while the solvent is less polar compared to silica.
The polar components of the analyte will adhere to the silica tightly and thus travel slowly up the plate, while the less polar or non-polar components will not adhere that strongly to the silica and travel up the plate relatively fast with the solvent. Now let’s again go back to the very first picture, discussed in this tutorial.
As shown above, the three components A, B and C of the reaction mixture travelled different distances, as the solvent moved up the TLC plate. Measured from the origin (where we spotted the reaction mixture): component C travelled 1 cm, component A travelled 2 cms and component B travelled 3 cms. The solvent travelled 5 cms (distance from origin to solvent front).
Rule of thumb:
  • The component that travels the least distance on the TLC plate is the most polar, since it binds to the silica most tightly.
  • The component that travels the maximum distance is the least polar; it binds to the silica least tightly and is most soluble in the non-polar solvent (mobile phase), and hence moves up the plate with the solvent.
So just by looking at a TLC plate, you can tell which component is more polar and which component is less polar. There is also a quantitative parameter, termed as retention factor (Rf) that can be calculated for every individual component and this value is very commonly used in the ‘world of chemical syntheses’. This value is invariably reported in manuscripts so that people who replicate the synthesis of a compound can verify that they too are getting the same Rf values for the same compounds.
Retention factor is defined as the distance travelled by the individual component divided by the total distance travelled by the solvent. ‘Lower the Rf value, more polar the component.’
ComponentDistance travelled by the component (cm)Distance travelled by the solvent (cm)Retention factor (Rf) of the component
C15RfC = 1/5 = 0.2
A25RfA = 2/5 = 0.4
B35RfB = 3/5 = 0.6
Based on the Rf values (as calculated above), component C is the most polar and component B is the least polar.

Want to join the conversation?

  • blobby green style avatar for user Sharanya Sinha
    How can I cite this page? I can't find the name of author or publishing date etc. It would be really helpful if I could cite the Khan Academy website!
    (36 votes)
    Default Khan Academy avatar avatar for user
  • blobby green style avatar for user Evan Broggi
    In regards to gas chromatography, isn't it better to say that the separation is based on the samples interaction with the stationary phase of the column rather than the samples boiling point?
    (9 votes)
    Default Khan Academy avatar avatar for user
  • spunky sam blue style avatar for user Hala A. Lashin
    Extraction...is it considered one of the types of partition chromatography ?
    (5 votes)
    Default Khan Academy avatar avatar for user
    • piceratops ultimate style avatar for user Isaac Deatherage
      No. Extraction is based on two liquid phases where they are separated based on an organic layer (nonpolar) and an aqueous layer (polar). One layer is the organic layer that floats on top of the other; the bottom layer is polar and can be bound to a solvent. IN the case of mixing oil and water, the oil floats (nonpolar organic phase) and the water sinks (aqueous polar phase). This is clearly different than "partition chromatography" because the latter is based on a solid phase (that one compound has some affinity or attraction to) and a liquid phase (that another compound has some affinity or attraction to). In extraction, the inside of the beaker would have to be coated with a stationary phase, but it is not. So, extraction is not partition chromatography. Also, we can tell by the out-right definition from the Meriam Webster Medical Dictionary: Partition Chromatography: "a process for the separation of mixtures in columns or on filter paper based on partition of a solute between two solvents one of which is immobilized by the substance in the column or by the paper." In extraction, one is not immobilized, but they separate based on exclusion from one another.
      (5 votes)
  • blobby green style avatar for user Robin Yoon
    For ion-exchange chromatography, (specifically cation exchange) would raising the pH of the buffer will cause the beads to become more negatively charged thereby strengthening the ionic interactions between cations and the beads? and conversely for anion exchange chromatography?
    (2 votes)
    Default Khan Academy avatar avatar for user
    • starky ultimate style avatar for user ♪♫  Viola  ♫♪
      In ion exchange, you don't change the charge on the beads of the resin. You change the charge on the analyte (for example a protein that you want to purify). So in a cation exchange where the beads are negatively charged, raising the pH causes deprotonation of the protein. The result depends on the pH of the buffer and isoelectric point of the protein.

      Let's say the protein has a pI of 6.5 (it's neutral at this pH).
      If your column is originally at a pH of 4, the protein will be protonated, so it has a +ve charge and sticks to the -ve beads in the column. Raising the buffer pH to 6.5 or higher deprotonates the protein, so now it's neutral (or negatively charged if you raised the pH a lot), which causes it to stop being attracted to the -ve beads. Now the protein will elute.

      Had this been an anion exchange, then you would start at a very high pH so that your protein is in its anionic form, and you slowly lower the pH to 6.5 so that it becomes neutral (or below 6.5 so it becomes positively charged) which causes it to not be attracted to the the positive beads.
      (6 votes)
  • duskpin ultimate style avatar for user Jackie Wille
    Is it possible to calculate the Rf for the techniques other than paper and thin layer chromatography? For example, for liquid column chromatography the solvent and compounds travel the full length of the column. Would you do something like (time for solvent to reach the end of the column)/(time for the compound to reach the end)?
    (4 votes)
    Default Khan Academy avatar avatar for user
  • duskpin seedling style avatar for user Dawud Islam
    Which type of chromatography is more helpful to use: thin layer or column
    (2 votes)
    Default Khan Academy avatar avatar for user
  • male robot hal style avatar for user shreypatel0101
    Difference between gas and column chromatography?
    (1 vote)
    Default Khan Academy avatar avatar for user
    • blobby green style avatar for user Miriam Pater
      A big one is execution: most column techniques are (as far as I know) done by hand, maybe attached to an automatic solvent dispenser, but relatively small scale.
      A gas chromatograph on the other hand is a large machine (look up a picture) containing an injector, a column, an oven to control the T of the column and a detector (not sure if it's attached or included). The capillary column is less then a mm wide, is between 10 and 150 m long and coiled. Despite the scale of the machine it is accurate for small samples (think; even trace elements at a crime scene small). Hopefully this helped a little!
      (3 votes)
  • blobby green style avatar for user ariadna.popescu
    Hi, could you please tell me what the illegal e-number is in chromatography? because some of my homework is about that but I don't really understand what it is, and I've tried googling it but with no success, it gives me things that are unrelated to this. I would appreciate it if you could help me.
    Thank you!
    (2 votes)
    Default Khan Academy avatar avatar for user
  • blobby green style avatar for user Tsehai Archer
    Importance of retention factor
    (1 vote)
    Default Khan Academy avatar avatar for user
  • blobby green style avatar for user Tsehai Archer
    Why does dye travel up a paper in chromatography
    (1 vote)
    Default Khan Academy avatar avatar for user