physics

Starting with very basic stuff here, the simplist units of atlernative matter look like rings. They have various types of subatomic particles that spin around the center, and the faster they spin the more energy the particle gives off. They are attracted to the center but cannot reach it, so it makes an orbit that looks like a ring. These are typically not large, but can be be bigger depending on the number of orbiting particles
(notation image here)

~bonds

the way bonds are formed is fundementally diffrent from typical chemistry. Because the orbiting particles are attracted to the center, so are the orbiting particles of another molecule. For this reason they will often crash into each other, but be unable to break through the orbit. In some cases, two orbiting molecules will be repeled by one another, forming a gap in the ring, with the right timing, two molecules can link togeter. Note that because of attraction to the center (which is also called a ghost nucleus, something is there, we just can't see or measure it) it is difficult for the molecules to become unlinked once they are in this state. An alternative molecule would bind to a typical one by having one of it's orbiter's also become a valance electron, but this is rare and can only happen with very small rings that do not spin fast

~Electric Charge

alternative atoms have the ability to be positively or negatively charged relative to others. Orbiting particles can carry either charge, but their attraction to the ghost nucleus seems to come from some other mechanism. The entire molecule is the average of the orbiter's charges, but it might not necacarily be balanced all the way around the ring (i.e. one half could be more positive than the other, and as it spins the positive region is moved around the orbit) Because of this mechanism, the charge that a bonded molecule is exposed to can change throught the orbit. Some compunds move continuously as the electric force changes.

~interactive charge

this is a second type of "charge" that alternative atoms can have. It dictates their liklihood of interacting with conventional matter. "X" is the variable given to molecules that are not interactive, and "Y" is the variable given to those that are. How this is done is not well understood, becuse scientific tools are usually made of normal atoms, and loose the abiltiy to measure anything as the interactive charge goes toward X. It is observed that the charge can be flipped