[Nicholas Lee (OP)]

.... levels changing as molecules come together, just a mystery to why this happens, and can it is something that can only be observed, but cannot be explained by science, in any way.
So what I am saying is these are effects that are behaviors of particles of light, and electrons, that can be observed, but not explained by science.
I am grateful for your help, anything helps even a few words.

[chiralSPO]

This is very well explained by science. I have pointed you in the direction of molecular orbital theory before. I suggest you take some time to read up on what is known about it. You obviously have the time and desire to learn about this topic.

Here are some links to get you started, depending on your learning style:

http://chemed.chem.purdue.edu/genchem/topicreview/bp/ch8/mo.html
http://www.ch.ic.ac.uk/vchemlib/course/mo_theory/
https://en.wikipedia.org/wiki/Molecular_orbital_theory