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I am reading the experimental section of a paper, and it states

[compound of interest] Isolated as a pale yellow oil after flash chromatography on silica gel, eluting with 1-2% EtOAc/pentane...

This is all this paper states in regards to the work-up procedure. I fully understand everything in this section except what is meant by 1-2% EtOAc/pentane. Does this mean that in total only 1-2% by volume of ethyl acetate is used compared to the amount of pentane used in the flash chromatography? This could also mean that a solution of 1-2% ethyl acetate in pentane was used throughout the entire run (which I find most likely). Which of these interpretations is most likely? Would this mean the author of the paper did not change the polarity of the solvent during chromatography and only use a 1-2% EtOAc in pentane solution?

Here is the DOI to the paper: 10.1039/c6ob01026a

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    $\begingroup$ This looks to me like a gradient starting at 1% EtOAc in Pentane and finishing with 2% EtOAc in pentane was used. Must be a very non-polar product. $\endgroup$
    – Waylander
    Dec 26, 2019 at 23:24
  • $\begingroup$ In another section of this same procedure, however, it states "eluting with 2% diethyl ether/hexanes". Would this suggest that the gradient starts at pure hexanes and is gradually increased to 2% in this case. In the case of my question above, would it mean we start with pure hexanes and gradually increase the gradient to 1-2% EtOAc/pentane? $\endgroup$
    – Eli Jones
    Dec 26, 2019 at 23:52
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    $\begingroup$ It is going to have the same outcome whether you start with neat hexanes or pentane and gradient to 2% EtOAc/Ether or start at 1%. This is a very shallow gradient for a very non-polar material. If in doubt start with neat hexanes/pentane and run a slow gradient to 2% EtOAc/ether and expect to collect a lot of fractions. $\endgroup$
    – Waylander
    Dec 27, 2019 at 6:52
  • $\begingroup$ As Waylander say, there shouldn't be any different outcomes operating according to your various interpretations. That is probably why they do not mention any gradient. $\endgroup$
    – Alchimista
    Dec 27, 2019 at 8:05
  • $\begingroup$ @Waylander How do you apply a gradient to a flash chromatography? That sounds very cumbersome to me, unless you have a machine that mixes and applies the solvent automatically. $\endgroup$
    – Karl
    Dec 27, 2019 at 9:42

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Based on OP's question, I tentatively assumed OP is a novice to the isolation of organic compounds using column chromatography. Thus I'd explain this question with as basis as possible.

This paper OP sighted is for the synthesis of 2$H$-chromenes (2$H$-benzopyrans). They can be non-polar to polar compounds based on the substitution on benzene nucleus. The paper describes a series of relatively non-polar chromenes. When you do organic reaction, you monitor the progress of reaction with TLC analysis. During that analysis, you can determine that what solvent should be the most suitable for the particular compound elution. That's how the authours have determined several solvents such as 1% ethyl ether/hexanes and 2% ethyl acetate/pentanes, etc. for different different chromenes.

Some of these chromenes have been isolated using just one solvent. For example, evidently, they have mentioned isolation of 7-Methoxy-4-methyl-2-propyl-2$H$-chromene, using flash chromatography on silica gel, eluting with 2% diethyl ether/hexanes solvent system (this means solvent made by 2 parts of diethyl ether and 98 parts of hexanes, by volume). Note that it would also mean that they might have used certain volumes of following systems: (1) pure hexanes; (2) 1% diethyl ether/hexanes; (3) 2% diethyl ether/hexanes; etc. However, expected compound has come out with only fractions eluted with 2% diethyl ether/hexanes (remember, you supposed to analyze all the fraction by TLC), which may have combined and further analyzed by spectroscopy to confirm the structure.

As in another data set, they have mentioned isolation of 5,7-Dimethoxy-2,2-dimethyl-2$H$-chromene, using flash silica gel column, eluting with 1-2% EtOAc/pentane solvent system.It would definitely mean that they should have used certain volumes of few solvent systems: (1) pure pentane; (2) 1% EtOAc/pentane; (3) 2% EtOAc/pentane; (4) 3% EtOAc/pentane; etc. However, their expected compound has come out with fractions eluted with 1% and 2% EtOAc/pentane (concluded by the fractions analysis by TLC).

Later Note: As commented by Waylander, these type of separation is called gradient elution. By the scale of reaction, total elution must not go over $\pu{100 mL}$ of solvent for each compound.

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  • $\begingroup$ Just to clarify, when I actually carry out the gradient elution for my compound I should gradually increase the polarity ABOVE what was mentioned in the paper. So in my case gradually increase the polarity to something like 3.5% EtOAc/pentane. Since I will be using about 28 fractions of about 12 mL each, this would mean that I should start with ~40 mL of pure hexane and increase the EtOAc concentration by 0.5% each run until I reach 3.5% EtOAc. I will, of course, be checking the TLC each time, but this will give me a good estimate of where I should expect my coupound. $\endgroup$
    – Eli Jones
    Dec 27, 2019 at 16:36
  • $\begingroup$ It you are using a fraction collector, you can program the gradient with volumes. $\endgroup$
    – Mathew Mahindaratne
    Dec 27, 2019 at 16:48

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