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Which recommender to ask?

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This is going to be a long post, so please bear with me and help me make a decision!

I am a junior at a liberal arts school and want to apply for a PhD at a top institution (Harvard, Caltech, WashU and the like) looking for some sort of combined organic-inorganic chemistry project. I will have a recommendation from the organic chemistry professor I worked with for 2 years, and if all goes well this summer, another one from a well-known inorganic chemist in a national lab I will work at over the summer. My problem is with the third one. I have several options, and I do not know which would help me or hurt me more!

Professor A: I had him for an organic and an inorganic class, and I did great in both! He is my favorite of these four, I see him most often, and he knows me best personally. He recommended me for the national lab. My main concern is that he has been here for only 2 years and already recommended 2 seniors who just decided for Harvard and Stanford, and I do not think I am quite as great as them. How would something like "this is the third or lower student out of the 100 I taught so far" sound?

Professor B: he is my academic advisor, and I had him for an inorganic class where I did very well. He also recommended me for the national lab, and I am supposed to regularly report to him my progress over the summer. He has had quite a few good students in his over 40 years teaching, but I still think I am one of the best.

Professor ? I did biochem research with her all freshman year, but I discovered that I don't like biochem that much. I also had her for a class and didn't do so great. I have a minor excuse for that, but I really don't think it's important enough for her to know. She turned out to be a great teacher, but not a great researcher, which is why she never had good students for research and I may be her best research student, despite being a freshman at the time. I would normally not ask her, but I heard that not asking someone you did research with might indicate that there were serious problems, which is not the case.

Professor ? I had him for a PChem class and later for a lab. I was the best in both, and he told me several times how much he enjoyed teaching me. He does mostly inorganic research and collaborates with some top schools. Once I randomly mentioned to him what happened to me in the class of professor C, and he encouraged me to ask any recommender to adress that, and said that he would address it if he had to recommend me. Another PChem professor says that he writes very strong recommendations for students who impress him much less than I did. But he is a little socially awkward, which is why most students and professors try to avoid him, and some professor pointed out that his collaborators might feel the same way, and a recommendation coming from him might actually hurt me.

Any opinions on which to choose would be appreciated!

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It sounds like you have some pretty good options actually.

It's great that you have 2 research recommenders in your field. Not many have that. Here are some points to think about, which I hope you might find useful:

1. Letters describing your research ability are the most useful. Your grades speak for your academic ability, but letters tell your research experience.

2. Being compared to current students at places you're applying to is a good thing. You might be selling yourself short, and Prof A might just write that you are just as good as the last 2 students who went to Harvard and Stanford.

3. At a lot of schools, 3 letters is the minimum, not the maximum. If I was sending 4 letters though, I would pick prof C and then one non-research letter (i.e. don't send more than one non-research letter).

4. You don't have to use the same people for every school. When you decide on the schools and faculty to apply to, send this list out to Profs A-D and ask if they think you would especially benefit from a their letter. Maybe they have collaborators/friends at one of the schools you're applying to, a former student of theirs went there, etc. A letter from someone connected to the school you're applying to is worth much more!

Actually the more I think about it, with only the information presented here, I would lean towards Prof C, because I really think research letters are much more important. You should talk to Prof C about your poor grade if you think they will mention in the letter. A letter from Prof C will also emphasize that you were doing research in your freshman year!

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