[Nicholas Lee (OP)]

It seems like a mystery how energy levels change in different atoms, and as atoms form covalent bonds to make molecules, electron energy levels change also.
As I see it there is three ways that make the electron change energy levels:
1. Energy levels are different in each atom, so is the amount of protons, neutrons a factor in the electrons energy levels.
2. As atoms form covalent bonds to form molecules, energy levels change also.
3. The further away the electron is from the nucleus, changes energy levels of the electron, as the electron is in higher shell levels.

So is this correct that distance from the nucleus, the amount of protons, and neutrons, and atoms forming molecules are all factors in electron energy levels changes.
If you knock a proton, or neutron out of the nucleus, I am not sure if the element changes to the next element up, or down in the periodic table, because it is now mussing a proton, or neutron.
But if the atom did not change to another element, by knocking out a proton, or neutron would the electrons, electron voltage change to a higher, or lower number.
I am grateful for your help, anything helps even a few words

[evan_au]

If you knock a proton, or neutron out of the nucleus, I am not sure if the element changes to the next element up, or down in the periodic table, because it is now missing a proton, or neutron.

You could take a stable atom like Oxygen ¹⁷O = 8 electrons + 8 protons + 9 neutrons.
If you knock out 1 neutron, this leaves behind the stable atom Oxygen ¹⁶O = 8 electrons + 8 protons + 8 neutrons.
See: https://en.wikipedia.org/wiki/Isotopes_of_oxygen#Stable_isotopes [Links inactive - To make links active and clickable, login or click here to register]

The electron energy levels of the two isotopes of Oxygen are pretty much the same.
There will be a bit of a difference in the infra-red spectrum, since vibrations of the molecule is affected the the mass of the Oxygen atom, not just the electron structure.

If you take ¹⁷O, and knock out one proton, you will be left with the unstable atom of Nitrogen ¹⁶N = 7 electrons + 7 protons + 9 neutrons.
Nitrogen has quite a different electron energy levels and spectrum than Oxygen.

However, because this Nitrogen isotope is unstable, it breaks down in about 7 seconds to Oxygen or Carbon.
See: https://en.wikipedia.org/wiki/Isotopes_of_nitrogen#Isotopic_signatures [Links inactive - To make links active and clickable, login or click here to register]

Unfortunately, the results of atomic colisions are a bit more random than this - sometimes you will knock loose an alpha particle (2 protons+2 neutrons) or a Beta particle, and often there will be gamma rays produced. So you end up with quite a mix of atoms in the result.

There are some problems with this approach to medical imaging:
- It takes enormous energy from a particle accelerator to dislodge protons and neutrons from the nucleus of an atom
- This is much more dangerous than taking an X-Ray or CAT scan of a patient
- The impact of the collision imparts a lot of energy to the nucleus, ripping it right out of the atom.
- The electrons do not make a smooth transition from the energy levels of Oxygen to Nitrogen. The energy of the collision scatters the electrons everywhere.
- The energy of the incoming particle beam and the debris from the collision is far greater than the binding energy of biological molecules: perhaps millions of electron-volts, not just 1-4 eV. This tears apart the biological molecules you are trying to study.

So while https://en.wikipedia.org/wiki/Nuclear_transmutation [Links inactive - To make links active and clickable, login or click here to register] does change the electron energy levels, it will destroy the biological molecules you are trying to study; if it doesn't kill the live patient immediately, it will give them radiation burns (or at least, cause so many mutations that it will give them cancer, eventually).

Nice try, Timemachine2!

[evan_au]

Perhaps a related, but more effective technique is to identify a molecule which sticks to the biological protein you wish to study (eg Tau tangles). You ensure that some of the atoms in this "https://en.wikipedia.org/wiki/Radioactive_tracer [Links inactive - To make links active and clickable, login or click here to register]" emit some low-level radiation.

You then give the patient an injection containing the tracer molecule, and wait an hour (or a day) for the tracer to stick to the target molecule. You put the patient in a radiation detector, and this provides a map of where the tracer occurs in the body. This indicates the presence and distribution of the target molecule (eg Tau tangles).

This has the advantage that:
- The accelerator beam does not need to dislodge a lot of atoms between the person's skin to where the  Tau tangles might (or might not) exist. The tracer goes direct to the Tau tangles.
- If there are no Tau tangles, the tracer is excreted from the patient's body.
- There is less radioactive debris inside the patient