How to nail a Ph.D. interview when the professors work is not a good fit with your background? I saw an offer for Ph.D. positions (USA) where 4 professors were on the list. I chose one (Prof X) and wrote my SOP according to his research and applied. 

Now another professor (Prof Y) from the list asked me for a skype interview. Now I am wondering how to nail this interview as I really want to get a position. 

Prof Y's work doesn't fit well with my background and my publications (so I was wondering if he just takes the interviews and selects students?)

If he asks me if I have any questions regarding his research, I am afraid I can't ask a smart question.

The email was kind of super positive where he wrote he is very impressed with my CV. I don't want to miss this chance at any cost. Is it ok if I tell him that I have a little knowledge about his work during the interview?
In the US this probably matters less than you think, though I don't know your field. In most cases, however, a research advisor isn't chosen at the time of acceptance, but later, maybe a lot later. First, you need to pass qualifying exams and before that, take whatever courses are necessary to enable it. If you are already prepared for those exams, then it is shortened, but still an essential step. 

So, you are normally joining a "department", not a specific PI's lab. It may well be that Prof Y is just handling lots of the interviews for the group of four and they are collectively looking for a group of good students to join. 

While it might be otherwise, the above is the normal thing in most fields in US. 

So, the fact that your research focus isn't the same as that of Y may matter little as long as you show you are prepared generally, that you are interested, and, perhaps, that you are flexible. The last can save you and get you in the door, after which you may have more options. 

It should be fine to say that you have more experience and even more interest with topic M than topic N if you are asked specifics. But it might be a mistake to say that you would never consider N. 

In other countries the situation is quite different and application is more commonly made to an individual professor than a department. 

But I was several years into doctoral study in math before I linked up with my research advisor. Though I entered with only a BA. 

In chemistry it might be a bit different, but only if the four professors ran separate labs, separately funded. But the fact that they advertise as a group, suggests not.