First, don't obsess about it. In chemical engineering, Science and Nature papers are rather rare, and probably even more so if you're doing theory. So, while a paper in those very high profile journals can give your career a great boost, not having one is not a career-breaker.
Now, if you want to know how to orient your research to things that get you a greater chance of being published in such venues, my first advice would be: do something you're excited about, something you think challenging and you want to address. If you enjoy solving the problems you work on, you'll do much better work and get a better chance of getting that shiny paper. Also, you might just be happier doing stuff you like, obviously, even if you don't publish it in Science.
However, it is true that some fields and subfields are over-represented in journals. This depends on journals, but very high profile journals tend to prefer:
- Hot topics. In your field, it used to be carbon nanotubes. Nowadays, I'd say “nano” is a good keyword, metal-organic frameworks are a widely published system. But… that's not entirely foolproof, because this will change and it's not certain that the choice you make right now will still be a hot topic in 4/5 years.
- Theoretical work that addresses very basic questions that are not yet fully answered: dynamics of water, the nature of the hydrophobic interaction, the Hofmeister series, that sort of stuff.
- Controversies, work that challenges common assumptions.
Oh, and if you make it, I claim co-authorship based on the above contribution!
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