Capital is lower after a couple of seconds (6)
I believe the answer is:
moscow
'capital' is the definition.
(capital of Russia)
'lower after a couple of seconds' is the wordplay.
'a couple of seconds' means two replacements for 'second'.
'lower' becomes 'cow' (something which lows - makes cow sounds).
'after' means one lot of letters go next to another.
'second' becomes 'mo' (both are short periods of time).
'second' becomes 's' (common abbreviation).
'mo'+'s'='mos'
'cow' put after 'mos' is 'MOSCOW'.
'is' is the link.
(Other definitions for moscow that I've seen before include "Olympic city, 1980" , "Kremlin location" , "Bolshoi Ballet base" , "City of 13" , "Russian city" .)