I think you need to get a clarification from your journal: .pdf can support raster images embedded (as can most vector output formats) and is often used in that manner in the print & publishing industry - if they will accept a .pdfwhich has embedded raster images, you need to find out what minimum resolution they need for their press' processing pipeline.
For your part, I hope like mad that your native files in DX Visualizer and Ligplot are resolution-independent so that you can active choose output pixel dimensions and hence resolution. I'd also add the thought that I hope very much that whatever you are using to do your page layout is vector based or at least a publishing tool, and not a raster image editor...
OP has updated question with sample images: they are very low resolution, and will either print incredibly small or will look terrible when printed. Is there a way with the tools at hand to get output from these at a far higher resolution - 3x higher at a minimum? If so, I suggest doing so, as otherwise, even when you succeed in giving the journal publisher .pdf output with your image(s) embedded, they will look less-than-optimal.