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So I'm building a character who works in a particular field of science and I found an e-mail for a scientist on the internet and emailed him. I described how I'm writing a sci-fi story and gave him some details to get him interested in the project. He replied and I asked about how things work in his field. (I emailed several questions and I'm yet to get a reply).

My question is, when researching in this way, should I tell people I'm building a character based on them and then interview, or pretend that I'm just interested about their field and wanted to ask a few questions out of curiosity?

"I'm just curious" is not a very compelling argument, especially when you're emailing a random stranger who's probably too busy to answer every such email that enters his inbox. "I'm writing a book", however... who doesn't want to have their story told in a book, or see something they're passionate about get adapted into a story?

Let me give you an example. Robot combat is one of my lifelong passions - I don't compete myself, but I'm pretty knowledgeable about it. If you were to ask me, "Hey F1, could you tell me a few things about robot combat? I'm just curious", I'd link you the Wikipedia article and some Robot Wars fights on YouTube, and answer any technical questions that I knew the answers to. If you were to say, "Hey F1, I'm writing a book about robot combat, could you tell me--", you would not be able to shut me up. _{And I'd be first in line to buy that book, but I digress.}

So yes, definitely mention that you're writing a book. It'll get the person engaged more.

As for "building a character based on them": I'll start by noting that just because you're using information from this scientist to create your character and his research, that doesn't mean that the character is actually based on him. Their personalities, appearances etc. could be completely different, they just so happen to work in the same field.

If in doubt, it's probably worth asking, "Is it okay if I base one of my characters on you?" As @hhhhhhhhhhhhh indicated in his answer, not everyone would be okay with that. If he isn't, you can just tweak your character until it's clearly distinguishable from the real person.

Speaking as a research scientist, I cannot really explain to you "how things work in my field."

What things? There are myriad things, like in any other profession. How to propose experiments, how to limit research, how to manage students, how to manage professorial duties besides dealing with classes and students, how to get on committees, how to propose collaborations, how to apply for funding, how to help students choose PhD research topics.

You have to limit your questions to specific things I can answer. I would propose you have a list of potential things you WANT to do in your story, and ask me if those are plausible, or not.

e.g. Could a researcher actually discover a new advanced form of AI, and keep it a secret, to make a fortune off of it privately? Yes. Unless she had collaborators, like other professors or her own graduate students, then the answer is likely No, not for long anyway. Research like that is just not compartmentalized in that way.

Pick things relevant to your story that you want to sound plausible, even to actual scientists, and ask about them. That will be entertaining to the scientist you are questioning. You can offer her credit as a consultant for certain questions you had within the story.

Do not try to base your character on her without written permission, as I commented above, you risk a lawsuit if you do. Professors are not generally wealthy, but they are upper middle class, and reputation is paramount in the academic fields; do not assume they won't protect themselves and their reputation.

Personally, as a scientist, I'd very much appreciate it if you were honest with me. I wouldn't want to be portrayed in a novel, and if you tricked me into "modelling" for you, I might sue you.

As a writer, I would use the knowledge about their field that my contact person gave me, but I would create my own character not from them but from what my story requires.

In terms of building a character, what should guide you is what the story requires. If you need a mad scientist to make Frankenstein's monster, but the person you meet is nice and well-spoken, do you then change your whole story?

It is not a bad idea to notice things about people, and incorporate them into the story when you need them. Habits, pose, movement, dress, verbal tics. For example, J.K. Rowling had an unpleasant teacher who had a preference for twee things. The unpleasantness bound with the style became a defining trait of Professor Umbridge. But the impetus to incorporate the particular person into the story came from the story, not the other way round. It's not until the 5th book that Umbridge comes in.

You can go to a professional for professional knowledge, that makes sense, but as far as being a person goes, we're all professionals in that. Why should you base your character on a guy you haven't even met yet?

There is another element in play: if you tell a person you're going to base a character on them, first they might not want this. They might well be concerned about how you represent them, want to maintain their privacy, or prefer to avoid this for some other reason. Second, if they don't mind, they might well be self-conscious during your interview, acting unnaturally. How does that help you write a character? Third, suppose you promise a person to base a character on them, but then for various plot reasons, you decide you need the character to be different. How are you going to explain that to the real person you've made a promise to? Fourth, suppose you base a character on the person, but then you need him to do something immoral - commit a crime, lie, create a monster, whatever. How do you think the real person is going to feel?

Note that most fiction books contain a disclaimer on the copyright page, along the lines of

All the characters in this book are fictitious, and any resemblance to actual persons, living or dead, is purely coincidental.

This is done exactly to protect you from all the trouble I've listed above (and more similar trouble). Which proves that there is trouble to be had with basing a character on a real person without their consent. (And of course, you cannot very well put such a disclaimer in your book if it's a lie.)

And yet another thing, though maybe this should go without saying. Do your homework before you meet a professional in person. Find out as much as you can about the subject you're going to be asking about, and prepare the specific questions you want to ask. The person's time is valuable. Don't waste it. If the hour you have with a scientist is spent on him explaining you the basics, you've gained nothing you couldn't have found yourself. If you already know the basics and can understand what he's talking about, you can use the time to gain an advanced insight that can make your story better.