When I'm running HPLC analysis using C18 column (5 μm, 4.6 × 250 mm) with a flow rate of 1.2 mL/min under isocratic elution mode, what is the best way to initiate and shutdown the flow rate. Should I activate/shutdown it at once or do it gradually i.e. by starting with 0.2 mL/min and increasing gradually?
Purely physical thinking I have always choosen to shut down in small steps. I believe it is better for the pump and for the packing of the HPLC column.
I do not know any report about this, but you could ask HPLC equipment manufacturers like Shimadzu and ask their opinion.
On a modern chromatography support it will probably not matter. You can gradually ramp it down from 1.2 ml/min to 0 ml/min over 20 or 30 seconds, or just set it to flow = 0 and you should be fine. Concerns about "shocking" the packing material were real back in the 1980's, but not of much concern going from 1 to 0 or 0 to 1 ml/min on a modern HPLC column with a silca type support.
My own personal way (because I initially learned to develop HPLC methods in the 1980's) is to drop it in steps, quickly from 1.0 to 0.500 to 0.100 to 0.0 over about 10 seconds, but you can just set it to 0 and let the pressure naturally bleed off (as it always will since the column buffers the change in pressure).
Just out of habit, I have my method programs ramp up in the prerun procedures and ramp down in the post run procedure so I don't have to even think about it. I doesn't really cost me anything if I automate it.
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