Restructuration of molecules.

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Do you think that after the 3d printer and atom colliders, we'll have the technology to restructure atoms to make, lets say, water out of hydrogen peroxide (H2O2) or even diamond and water out of glucose (C6H12O6) ?

The hydrogen peroxide --> water + oxygen reaction happens naturally. It occurs with sunlight, specifically UV energy, cleaving the oxygen-oxygen bond to start the reaction process. That is why hydrogen peroxide is stored in dark containers to prevent the reaction when it is not needed. Certain biological catalysts (enzymes) can also start the conversion reaction on hydrogen peroxide. That is why hydrogen peroxide bubbles when put on a wound, as enzymes would be present.

As for converting glucose into diamond + water (steam), it can be done now if just enough heat and pressure are applied in a particular way. Catalytic materials can help give the crystals a stable medium surface to grow on. Any carbon source (including human ashes) can be used to make synthetic diamonds, but higher carbon content makes the process easier to do as there would be less impurities to deal with. It will not result in large gem quality diamonds, but either microsized crystals or diamond thin films that layer the inside surface of the container. One of the first synthetic diamonds made was out of peanut butter as the carbon source:

http://www.wisegeek.org/can-peanut-butt ... youknowout

If you are asking: Will we ever be able to build complex molecules out of single atoms using a special printer, without using chemical reactions in the process? It could be done with the chemical reactions, but I do not know how it could be done without them. I have friends who work on 3-D printers and have been actively looking into modifying a 3-D printer system for biochemical experiments that I want to try with it.

I am happy that you are thinking about this process, as it could lead you further into the world of chemistry, something that I highly recommend. Please let me know if you have more questions and I will be happy to help answer them.

3D printing is not at the scale of atoms.

3d printing is generally an additive process typically using extrusion of polymers. Some case the polymers are cured by light/laser in other case it is thermoplastic used and it just cools.

Also ceramic powders can be bonded to form layers.

Most 3D printing happens with a series of layer in a single plane. This is not the only way but the most common.

Sounds like alchemy to me. Maybe you could make a Philosopher's Stone with one.

We probarbly could, but it likely won't be practical in 90% of the situations. don't expect star-trek 'replicators' anytime soon

If viewed from perspective of Centuries, the exponential progress toward the above is instantaneous, but Dogdamn it sure feels slow to me.