To answer your question, you should NEVER misrepresent your goals. This could lead to you possibly entering a program that you have no interest in completing, which is arguably worse than not getting into a graduate program at all.
Since it seems you now have a much clearer idea of what you want to do, look for programs that accommodate your interest in computational biology/chemistry and explain in your personal statement what inspired you to abandon the work you were previously doing.
If it helps, my major research project as an undergraduate investigated fern ecology, but I'm going into a Biochemistry PhD program that is more in line with my core interests, namely chromatin-mediated gene regulation and other topics in epigenetics. It may have helped I did some biochemical research one summer and cell biology during an REU, but I don't think the fact my major project was totally unrelated hurt me. Considering I'm where I want to be, it all worked out.
Does your institution have an introductory bioinformatics course you could take? I took one semester of bioinformatics; it covered how all of the next-gen sequencing technologies work while also introducing me to Python, command line, and the general principles of bioinformatics.
Overall, I don't think your odds are that bad so long as you communicate your change of focus in your personal statement.