In developing a PUI research program it is critically important to 1) keep in mind who you are working with, 2) your equipment and instrumentation resources, and 3) your own sanity. And if you want funding make it transformative.
We synthetic folks tend to get very focused on making specific molecules and can forget about the bigger picture of the science we create. If you are not careful the only science you move forward is how to make some obscure molecule in a new way. This can be of value to the other person in the world who wants that molecule, but may not be fundable since there is only one other person in the world who will benefit from your work. If have seen many early career faculty get funded only to then fall into the trap of only making molecules. Once the New Faculty bloom is off the rose they find the molecule maker has very limited funding opportunities.
In my opinion, to be transformative a project must make the reader of the grant or paper think that the results in some way change their perspective on the broader field. The extent to which it changes the perspective will/should dictate the reviewers evaluation of the work. Every time I think about my own projects I catch myself asking, where the hook is. I can come up with very cleaver ways to make molecules, but if they don't have a element that helps us understand organic molecules better to give us a new general tool for the toolbox I can't get funded.
As a synthetic organic person I don't think we can find federal funding to just to make molecules. There may be some speciality pharma or industrial application that might make your targeted synthesis fundable, but those sources have been hard for me to find and fall outside our "transformative" discussion. The synthetic project must break new ground or at least tell us something about the ground that has previously been covered that enables us to rethink the earlier ideas about the chemistry.
You have to have an idea, and as organic chemistry has become a mature science over the last fifty years, the transformative ideas get harder to find and exploit. I have come to believe that you need to develop a bigger picture question that you will develop expertise over a lifetime rather than going after the method or molecule of the day. If your interest is, for instance alpha-hetero anions, you can explore the fundamental nature of the beast, methods to make them and their application in synthesis. Having a range of things to do will allow you to tailor the projects to the students you have and allow you to establish your own reputation within the field.
One of the challenges for the PUI researcher is not just developing a transformative idea, but one you can move forward at a reasonable pace. Undergraduates will typically spend less than ten hours per week doing anything that is actually useful. (Some would say, far less than ten hours.) So your project plans must take their time and skill into account. In their early days of their development students can generate data. Research programs that need data to study a mechanism or looks at the influence of a variable on yield or selectivity are manageable. Plus getting numbers and making a table or graph helps the student gain confidence. If the trends seen by these students can inform the synthetic work and add to the general understanding of the topic under study there can be pubs and presentations which will support the program at grant time.
PUI's have limited resources and in tough economies start-up packages tend to shrink. In looking at schools check out the instrument holdings and when you interview find out about the upkeep and condition of the instruments you will need. I have had to upkeep just about every instrument I have ever used in the lab, and have see the guts of NMRs, GC, GC-MS, HPLC, Stirrers, Hotplates, etc. Instrument upkeep can become the black hole that sucks up all your lab time.
Don't despair if resources are limited. I have made many trips to RO1 institutions to use libraries and instruments. What your school lacks a neighbor might have. If you develop a collaboration with an RO1 partner you might be able to bypass much of the cost of using instruments on that campus.
In protecting your sanity I will remind you that teaching and service will absorb much of your time. You will not have as much lab time as you think. At the same time without you in the lab your students will wander around pouring expensive reagents into waste bottles and breaking glassware for amusement (maybe not, but it seems that way). You need to develop project that don't require your expertise.
Lastly, a word for those preparing to enter the job search in the Fall. Develop your idea now! Start thinking about funding sources. Start writing your research plans now. August will be here before you know it.
T. S. Hall