First of all, what's a prepositional verb? A prepositional verb is a verb followed by a preposition, where the meaning is dependent on the combination of both items. For example :
He's looking after the children today.
He's looking for a new secretary.
He's looking into the problem.
In none of these sentences does it make sense to ask What does "look" mean? On it's own, it means nothing. The meaning is formed through the combination of the verb and preposition (look after = take care of; look for = try to find; look into = investigate).
So, if you change the preposition in any of these sentences then the meaning of the whole verb changes.
Now consider the following sentences :
He looked into the box, but couldn't find anything.
He looked behind the box, but couldn't find anything.
He looked under the box, but couldn't find anything.
Here look is not a prepositional verb. It's an ordinary verb with its own meaning - look = direct your gaze. And this doesn't change regardless of what preposition is used. The preposition simply introduces a prepositional phrase telling us the direction of the gaze, which could be any direction at all.
In addition, the prepositional phrase is an optional component : He looked, but couldn't find anything. That's not true of the sentences with prepositional verbs.
So - not every verb which happens to be followed by a preposition is a prepositional verb. Test yourself to see if you've understood : which of the following are prepositional verbs (answers below).
1. It took me ages to get over the 'flu.
2. We had trouble getting into the house.
3. I ran into David in the market.
4. She ran round the park.
5. He really takes after his father.
Not every verb + preposition combination is quite as clear cut as this. There are some cases where the preposition is not totally interchangeable, but on the other hand does not alter the meaning of the verb. For example :
He applied for the job.
Can you change the preposition here? Obviously, if you want to continue the sentence with the job, then no. The preposition is dependent on the verb - it doesn't have an independent meaning - and for this reason this sort of combination is generally classed as a prepositional verb (see eg Leech and Svartvik 1975). But consider the following :
He applied to IBM, but didn't get an interview.
He applied several times, but didn't get an interview.
Whether apply is used with a different preposition, or with no preposition at all, the meaning of the verb remains the same - and as we saw above, that can't happen with our "pure" prepositional verbs. I'd therefore argue that these verbs fall into the category of verb + prepositional phrase, rather than of prepositional verbs.
Leech, G and Svartvik, J (1975) A Communicative Grammar of English, Longman
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Answers : 1/3/5 = Prepositional verbs