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Imagine I synthesize and characterize a molecule for the first time, but for which I also do not know if it has any application. Is this, under EPC, patentable?

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Not in the US due the "useful" requirement. In the rest of the world they have a requirement for "industrial applicability" so I imagine the answer in the EPC is "also no. I heard a patent attorney teaching a class say "pore it on the grass, it might be a herbicide or a plant growth enhancer. Or maybe it peels paint." –  George White May 25 at 1:43
That's exactly what I thought. Still, it would need to demonstrate herbicide activity, right? –  TMOTTM May 25 at 7:30
Chemical patents are a sub-cult of mystery to me. I believe you need to cite experiments you have done demonstrating usefulness, they frown on claiming the chemical is good for manipulating another chemical that, in turn, has no use. And it not good to say it cures everything. –  George White May 25 at 16:51

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EDIT: In hindsight, I fear I might have answered the wrong question. Too late to retract now I suppose.

An approach I have seen people use is to analyze the chemical properties and guess at what it might be used for. Is it aryl? Improved perfume synthesis! Does it have nitrogen next to benzene? A new way to synthesis drugs.

Brainstorming in this way can often lead you to both casting a wide net and find applications. All you need is one use case and then they explode by being inter-related.
The new process of synthesizing the chemical is patentable. You still need the useful angle, but I am sure you had that in mind when you started? (Why would you just randomly invent something that costs $100k of dollars without a purpose?)

Polymer patents also are very much based on "I set out to make a chemical with variable properties X Y and Z on range of blah blah blah by varying A B C from here to there, and this is how I make it." Suddenly you have locked out a large application area, an industrial process, and set ridiculously broad ranges that are unreasonable and block anyone else from entering. (This would theoretically apply to your process patent as well.)

As far as the scientific scrutiny part goes, the art of BS'ing and telling a good story goes a lot further than the data. The data part comes 2 years later after the initial filing. Plenty of time to, uh, tweak the results.

Now I am no lawyer, but I can tell you this is how the big companies do it.

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