I think the concept is workable, but the whole electrons and protons thing is not.
I'd look at minor creation and similar spells and create a power with similar wording etc.
Hmm...
I suppose you're right, I suppose i didn't consider the long reaching effects futher than the few examples i had thought of.
Alright, scraping this domain for something else, I'll try to think of something more reasonable. Unless i put some heavy restrictions to balance such a powerful ability.
Thanks for the voice of reason
Its not that its powerful (though it absolutely is), its that 99.999% of things that players will attempt to do with this ability will have no rules backing behind them and will require DM adjudication. It also suffers from the "Sacred Geometry" problem of paralyzing the game while a player consults their chemistry textbook or the internet mid combat to determine if transmuting 25kg of oxygen from the air into carbon will cause the room to become a hypoxic environment based on OSHA guidelines. Or arguing with the DM for 30 minutes about the ability damage caused by chlorine gas, or if it should be a nauseating effect, or a blinding effect.
An ability like this may work OK in a much more freeform RP system, but in a system with heavy codification like Pathfinder, its never going to be a good fit.
Interesting idea though!
If you want to do this I recommend you limit yourself to adding/removing electron/proton pairs so that you maintain charge neutrality.
Pick a very limited set of changes: I.e. can transform up to 5kg of base metal (iron, tin, bronze, lead, ?) into another base metal. Cannot transform enchanted items. Items carried or held receive a saving throw [Fort or Will of the bearer]. Item must be separate; if it is mechanically attached to any other base metal, there is a concentration check (DC based on ?) or the attempt fails. You cannot transform part of an item.
This is a much better approach. It doesn't require a sophisticated knowledge of atomic science that is absurdly unrealistic for a medieval setting. (In Golarion, I wouldn't expect anyone outside the Technomancers of Numenara to even know what a proton is, much less how to apply that knowledge to perform subatomic alchemy.) And more importantly, it puts things in terms of established game mechanics, especially if you use the rules in Ultimate Combat for weapons and armor of unusual materials (softer metals gain the fragile property, for example).
Just be careful to keep this domain power balanced against what spells like versatile weapon and polymorph any object can do at the same caster level.
Oh, and another thought: All Pathfinder cleric domains grant one power that is gained at 1st level, and a second power gained at 4th, 6th, or 8th level (depending on how powerful it is). This domain should follow that two-tiered model as well.
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Making the changes temporary, and having them primarily affect the hardness/hit points of an item (temporarily transmuting them into a more durable or less durable material) could be one way to go. Other options could tweak a suit of armor or weapon to make it function as armor one class heavier or lighter, or a weapon as one size class larger (by increasing it's density) or smaller (by decreasing it's density), which could be either a buff or debuff (making someone's breastplate heavier and function as 'heavy armor' when they don't have heavy armor proficiency would be an effective debuff, for example, while making a breastplate lighter could allow them to move faster). Give it a touch range and a duration of rounds per level, and it should be roughly similar to various other 1st level domain powers (i.e. mostly useless at 1st level, but situationally usable at higher levels).
At 6th or 8th level, more specific changes could be made, turning weapons or armor into silver, cold iron, mithril or adamantine, for a short time, for instance. Other materials and options could also be possible, turning wood into darkwood, for example, but many 'special materials,' such as dragonhide, or other skymetals, would be out of the question, as the effect either doesn't fit the flavor (dragonhide, for example) or the effect might be too hard to adjudicate / balance (skymetals, planar metals, etc.). That's assuming just materials changes.
Actual shapechanging of objects could turn a weapon or armor item into any other weapon or armor of the same type/class (light, two-handed, medium, heavy, etc.), but that might be getting a little bit too complicated for a single power.