There's no such thing as the temperature of a molecule. Temperature and pressure are both outside-world manifestations of the energy the molecules have. But on the molecular level, what it is is the kinetic energy with which they're all scurrying around.
When the fuel/air mixture is compressed during the compression stroke, the temperature is raised to the flash point of the mixture. The work done during the compression pumps energy into the molecules, their kinetic energy increases, and they begin scurrying around fast enough so that when they collide, they're able to stick together, form a new molecule, and release some of their kinetic energy in the form of heat.
