Ōnoki (Naruto) using Dust Release/Particle Style to manipulate molecules.
Sentry (Marvel Comics) destroying the molecules of Molecule Man...
...and learning he has control over molecules.
In his Ultra form, Sonic (Archie's Sonic the Hedgehog) has power over local molecules and atoms...
...as he demonstrates by converting air to water with a thought.
Bender Bending Rodríguez (Futurama) reached atomic scale, allowing them him to manipulate water and CO2 molecules to create alcohol.
Maxwell (Valkyrie Crusade) is a arrogant devil that can control molecules.
Bill Cipher (Gravity Falls)
Blue Marvel (Marvel Comics)
Like Chase, Skylar Storm (Mighty Med) can use this ability in conjunction with her Molecularkinesis to make thing explode, render organisms immobile, and even turn her white highlights of her hair pink to hide her evilness at a greater scale than Chase.
Chase Davenport (Lab Rats) can use his Molecularkinesis in a similar way as it superpower cousin but with more limits. He can lift object, complete stop them, and even immobilize people, thus canceling out users with super speed.
Lexi Krane (Lab Rats) has an ability that is similar to Chase's molecularkinesis but instead she changes the said object on psychical contact, like she turned a metal chair into ice and then melted it.
Patty/Patty Putty (Superhero Kindergarten) can rearrange her own molecular structure to that of stretchy and bouncy putty