About good hardware for ChemDoodle 3D, you should first observe the application when it runs.
You have a multicore machine. Let ChemDoodle run heavily, open the task manager with Ctrl-Alt-Del (for Windows, or find use the local equivalent). Does ChemDoodle use all cores? Does it occupy all the Ram? This tells you if more cores or Ram bring something, or as opposed, if a machine with few cores and faster clock would be better. Check also if ChemDoodle puts heavy load on the graphics card, because Cuda allows science computations on it; software exists to show the workload on the graphics card, whose computing power varies hugely among the models.
The Ram throughput matters generally more for science than the computing power, at a graphics card even more. Try to reduce the Ram clock in the Bios and measure if ChemDoodle gets slower. If the Ram throughput matters, then fast DDR4 is better than slower DDR3 better than DDR2, and more Ram channels are better. You can get used Xeon on socket LGA 2011 for very little money presently, they have 4 channels of up to 2133MHz DDR4 and 2 to 18 cores.
I didn't find quickly whether ChemDoodle uses SIMD instructions (AVX-512, AVX-256, SSE, or long ago MMX). As it puts no requirements nor suggestions on the CPU, probably it doesn't. Then, an old CPU like a Wolfdale is just as good as anything recent.