Perturbation with doctrine in time (6)
I believe the answer is:
dismay
'perturbation' is the definition.
'doctrine in time' is the wordplay.
'doctrine' becomes 'ism' (suffix for disciplines or schools of thought).
'in' means one lot of letters goes inside another.
'time' becomes 'day' (day is a kind of time**).
'ism' placed within 'day' is 'DISMAY'.
'with' acts as a link.
(Other definitions for dismay that I've seen before include "Alarm, distress" , "Feeling of surprise and discouragement" , "Consternation, disheartenment" , "upset" , "Consternation, distress" .)