As I understand it, this is not really how most practical materials research is done today. Bridging the "scale gap" between nano-scale research, micro-scale research, etc. up to something the size of a foundation for a skyscraper is very hard (read: almost impossible) right now. Those nano-scale research areas are pretty siloed and only in extreme cases like transistor manufacturing is there any meaningful overlap with production use cases.

In general, materials researchers for something like concrete are going to be better off exploring the (very large!) high dimensional space of possible formulations of existing concrete ingredients and pushing out the pareto frontier for the best possible concrete that way. Also, one probably shouldn't be using bleeding-edge concrete tech for a skyscraper foundation - in a safety critical application like that you just build it 1.2x bigger than you need and it'll still be much cheaper and safer than a process like what you just described.

Materials research is super interesting, though, even if it's not building up from quantum-particle scale research. And atomic / molecular features of inputs can yield interesting material candidates.

Source: I work (as a software dev, not a materials researcher) at Citrine Informatics, selling software to assist companies who are trying to do practical materials things like make better concrete.

Your metaphor simply doesn't reflect the reality.

Material sciences, condensed matter physics, chemistry and etc work up from the abstraction layer of "atoms". It's a quite well defined and relevant layer. So, until that work brings some different configuration¹ for atoms, they will have no impact at all.

1 - It doesn't need to be as new elements, but even for the resonance between the nucleus and electrosphere they didn't create anything new, and only things affecting the electrosphere matter. (Even then, they didn't create anything new on a nucleus either.)