what is happening in chemical reactions at a molecular level ?
In general, for two molecules to react, they must collide, in the right orientation, and with sufficient kinetic energy to overcome their natural electron cloud protection.
So, here come two molecules, and bash into each other, hard; their electron clouds sense each other as they interpenetrate, and discover that they can rearrange around the particular atoms or molecules such that something -- either two different molecules, or a single molecule, or more than two molecules, come out from the collision.
All the rest of chemistry is just recognizing the patterns of chemical bonds in molecules and how they can react, and also calculating the energies of the bonds in the starting materials (reactants) vs. the energies of the bonds in the products (this tells you how likely the reaction is to stay as reactants or to go to products, for particular reaction conditions (temperature, pressure, solvents, etc.).